Products for DNA Research2020 Catalog

glenresearch.com

Oligo synthesis success. The first time and every time.

INTRODUCTION

5ABOUT USCATALOG

5
6

STERLINGQUALITY AND PERFORMANCE ASSUREDAPPLIED BIOSYSTEMS INSTRUMENTS
STERLING CE PHOSPHORAMIDITESSTERLING SOLVENTS/REAGENTS
STERLING SUPPORTS
ABI 3900 POLYSTYRENE MODIFIER COLUMNSEXPEDITE™ INSTRUMENTS
STERLING CE PHOSPHORAMIDITESSTERLING SOLVENTS/REAGENTS
STERLING SUPPORTS

7
7
8
8
8
9
11
12
12
12
13

DNA PHOSPHORAMIDITES - SPECIAL PACKAGING

15

MERMADE INSTRUMENTS

16

STERLING CE PHOSPHORAMIDITESSTERLING SOLVENTS/REAGENTS
STERLING SUPPORTS
ÄKTA OLIGOPILOT
STERLING CE PHOSPHORAMIDITESSTERLING SOLVENTS/REAGENTS
DR. OLIGO INSTRUMENTS
STERLING CE PHOSPHORAMIDITESSTERLING SOLVENTS/REAGENTS
STERLING SUPPORTS
OLIGONUCLEOTIDE PURIFICATION
K & A INSTRUMENTS
STERLING CE PHOSPHORAMIDITESSTERLING SOLVENTS/REAGENTS
STERLING SUPPORTS
ALTERNATIVE PROTECTING GROUPSDEPURINATION RESISTANT CE PHOSPHORAMIDITESULTRAMILD CE PHOSPHORAMIDITESULTRAMILD SUPPORTSULTRAMILD SOLVENTS/REAGENTS

16
16
17
18
18
19
20
20
20
21
21
22
22
23
24
26
26
27
27
27

ULTRAMILD DNA SYNTHESIS27

SUPPORTS

28

GLEN UNYSUPPORTGLEN UNYSUPPORT FC
UNIVERSAL SUPPORT III
Q-SUPPORTS
HIGH LOAD CPG
REAGENTSALTERNATIVE SOLVENTS/REAGENTS
CSO FOR NON-AQUEOUS OXIDATIONUNICAP PHOSPHORAMIDITEBACKBONE MODIFICATIONMISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGTABLE OF CONTENTS

28
29
30
31
33
34
34
36
36
37

1

			

TABLE OF CONTENTS
SULFURIZING REAGENTS
5’-CE PHOSPHORAMIDITES
5’-SUPPORTS
METHYL PHOSPHONAMIDITESPACE PHOSPHORAMIDITESMETHYL PHOSPHORAMIDITESULTRAMILD SOLVENTS/REAGENTS
H-PHOSPHONATE MONOMERS
H-PHOSPHONATE REAGENTS
BETA-L-DNA MONOMERSLOCKED ANALOG PHOSPHORAMIDITES

37
38
39
40
41
42
42
43
43
44
45

OLIGONUCLEOTIDE-DIRECTED MUTAGENESIS

46

TRIMER PHOSPHORAMIDITES

46

DUPLEX STABILITY MODIFICATION

50BASES AFFECTING DUPLEX STABILITY
ZIP NUCLEIC ACIDS (ZNA®)
CDPI3 MGB™ LABELING
SELECTIVELY BINDING COMPLEMENTARY (SBC) OLIGOS
UNNATURAL BASE PAIRSCAPS FOR INCREASED DUPLEX STABILITY AND BASE-PAIRING FIDELITYEPIGENETICSDNA METHYLATION

54
54

PCR/SEQUENCING APPLICATIONS

55

DUPLEX EFFECTS
Tm MODULATION
CLEANAMP® MONOMERSCHAIN TERMINATORS

55
57
58
59

STRUCTURAL STUDIESSTRUCTURE/ACTIVITY RELATIONSHIP
HALOGENATED NUCLEOSIDESDNA DAMAGE/REPAIR
CLICK DNA AND RNA LIGATION
5’-LABELING OF MicroRNAs
2’-5’ LINKED OLIGONUCLEOTIDESMUTAGENESISIN SITU SYNTHESIS OF DNA ANALOGSPROBING DNA STRUCTURE WITH FLUORESCENT NUCLEOSIDESPHOTO-REGULATION OF DNA FUNCTIONINHIBITION OF DNA METHYLTRANSFERASESLARGE SCALE SYNTHESISNON-CANONICAL STRUCTURES
G-QUADRUPLEXTRIPLEX-FORMING OLIGONUCLEOTIDES
i-MOTIF DNA STRUCTURESAPTAMER DEVELOPMENTMODIFIERSTERMINUS MODIFIERS
SEQUENCE MODIFIERS
3’-MODIFIERS
CHEMICAL PHOSPHORYLATIONALDEHYDE MODIFICATIONSPACER MODIFIERS
DENDRIMERS
BRANCHING PHOSPHORAMIDITE
PHOTOCLEAVABLE MONOMERSCONJUGATION USING CLICK CHEMISTRYOLIGO-CLICK KITS
COPPER-FREE CLICK CHEMISTRY

2

50
52
52
52
52
53

61
61
64
65
68
68
69
70
71
72
74
75
75
76
76
76
76
77
78
78
81
83
86
87
88
89
89
90
91
94
95

TABLE OF CONTENTSSERINOL REAGENTS FOR MODIFICATION AND LABELINGCOT SERINOL PHOSPHORAMIDITEDABCYL LABELINGBIOTIN LABELINGFLUORESCEIN LABELINGFLUORESCEIN LABELING (SIMA)CYANINE LABELINGELITECHGROUP DYES AND QUENCHERBLACK HOLE QUENCHER DYESBLACKBERRY® QUENCHER (BBQ-650®)
RHODAMINE (TAMRA) LABELINGACRIDINE LABELINGDNP LABELINGCHOLESTEROL LABELINGTOCOPHEROL LABELINGSTEARYL LABELING
N-ACETYLGALACTOSAMINE (GalNAc) LABELINGCDPI3 MGB™ LABELINGMGB ECLIPSE® CPG
PSORALEN LABELINGEDTA LABELINGFERROCENE LABELINGMETHYLENE BLUE LABELINGLABELING WITH THIAZOLE ORANGELABELING WITH POLYAROMATIC HYDROCARBONSPUROMYCIN CPG
LABELING WITH METAL CHELATESLABELING FOR PHOTO-REGULATION OF OLIGONUCLEOTIDESQUENCHED AUTOLIGATION (QUAL) PROBESLABELING WITH ULTRAFAST PHOTO CROSS-LINKER
RNA SUPPORTS
RNA SUPPORTS FOR 3’ MODIFICATIONRNA SYNTHESISTOM-PROTECTED RNA PHOSPHORAMIDITESRNA SUPPORTS FOR TOM RNA SYNTHESISTBDMS-PROTECTED RNA PHOSPHORAMIDITESRNA PHOSPHORAMIDITES - SPECIAL PACKAGINGULTRAMILD TBDMS RNA PHOSPHORAMIDITESTBDMS RNA SUPPORTSULTRAMILD SOLVENTS/REAGENTS
MINOR RNA BASESMINOR RNA PHOSPHORAMIDITES (TOM PROTECTED)RNA SEQUENCE MODIFIER (TOM PROTECTED)MINOR RNA PHOSPHORAMIDITES (TBDMS PROTECTED)MINOR RNA TRIPHOSPHATES
2’-OME-RNA SYNTHESIS
2’-OME-RNA PHOSPHORAMIDITESULTRAMILD 2’-OME-RNAULTRAMILD SOLVENTS/REAGENTS
2’-OME-RNA SUPPORTS
MINOR 2’-OME-RNA PHOSPHORAMIDITES
2’-OME-THIOPHOSPHORAMIDITES
2’-MOE-RNA PHOSPHORMIDITES
2’-MOE RNA PHOSPHORAMIDITES
2’-F RNA SYNTHESIS
2’-F-RNA PHOSPHORAMIDITES98

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGLABELING

98
101
102
103
106
109
110
112
114
116
117
118
118
119
119
119
120
121
122
122
123
123
124
125
126
126
127
127
128
128
129
129
130
130
130
132
132
133
133
134
135
135
136
137
140
141
141
142
142
143
144
145
146
146
147
147

3

			

TABLE OF CONTENTS
2’-F ANA SYNTHESIS
2’-F-ARABINONUCLEIC ACID (2’-F-ANA)
2’-OME-RNA-PACE SYNTHESIS
2’-OME-RNA-PACE PHOSPHORAMIDITESPURIFICATION
GLEN-PAK™ PURIFICATIONPOLY-PAK™ PURIFICATIONGLEN GEL-PAK™ DESALTING
OLIGO-AFFINITY SUPPORTPHYSICAL DATAPHYSICAL DATA

148
149
149
151
151
153
154
155
156
156

INDEX

166

GENERAL INFORMATION

176

ORDERING
DISCOUNTSTERMS AND CONDITIONS OF SALEPATENTS

4

148

176
176
176
176

INTRODUCTIONMISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGABOUT USGlen Research develops, manufactures and markets reagents for oligonucleotide synthesis, modification, labeling andpurification. The company serves customers worldwide involved in basic research, diagnostics and therapeutics. Although
Glen Research’s original mission was to provide state-of-the-art reagents to researchers, the company also began offering
standard reagents for oligonucleotide synthesis but with the innovation that every batch was accompanied by a Certificate
of Analysis. The analytical techniques and quality criteria used for the evaluation and acceptance of these reagents were
to become an industry standard years later.  The company is headquartered in Sterling, Virginia. A privately held company,
Glen Research was acquired by Maravai LifeSciences in December 2017.

OVER 30 YEARS OF ASSURED QUALITY FOR OLIGO SYNTHESIS
1987

Glen Research was incorporated in the Commonwealthof Virginia

1993

Glen Research introduced the Sterling line of products,
a new standard of quality for oligonucleotide synthesis

1996

Company negotiated an exclusive license with Gilead
Sciences to supply C5-propynyl pyrimidine nucleosides
and G-Clamp phosphoramidites

1999

C o m p a ny awa rd e d p ate nt s fo r a c h e m i ca lphosphorylation reagent compatible with DMT-ON
purification

2003

Glen Research negotiated an agreement with GE
Healthcare Biosciences Corp. to supply Cyanine Dyes
to the research market

2006

In collaboration with Berry & Associates, Inc., Glen
Research awarded patents for pyrrolo-C analogues  
(fluorescent C analogues).

2013

In collaboration with Nelson Biotechnologies, Inc.,
company awarded patent for serinol phosphoramidites
and supports

1991

Company awarded SBIR grant for the investigationof large scale oligonucleotide synthesis using
H-phosphonate chemistry

1995

Glen Research negotiated an exclusive agreement to
supply 5’-biotin phosphoramidite worldwide

1997

Glen Research moves into a custom built building in
Sterling, Virginia

2002

Company made an agreement with Epoch Biosciences,Inc. to supply their proprietary dyes and nucleosides
to the research market

2004

Company awarded patents for a truly universal support
for oligonucleotide synthesis - US III.

2008

Glen Research obtained a license for the sale of Glen
UnySupport from Ionis Pharmaceuticals

2017

Glen Research is acquired by Maravai LifeSciences

2019

Glen Research receives its ISO 9001:2015 certificationfor Quality Management Systems

5

INTRODUCTIONCATALOG
OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI andother instruments.  If you would
like another type of vial/column
add the following to the end of
the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials
and columns for other instrument
types.)

6

Welcome to the Glen Research Catalog containing the most complete selection of products for DNA and RNA research.  
The Table of Contents at the beginning and the Index at the end of the Catalog are the most comprehensive we haveproduced.  There are always limitations to printed catalogs in a fast-moving technology sector and a complete and up-todate catalog is also maintained on our web site.
All minor bases, modifiers and RNA products are packaged for Applied Biosystems instruments.  We can provide vials andcolumns for a wide variety of other instruments.  As shown in the table to the left, we can accommodate catalog numbers
for unusual products to fit all popular instruments.  The table to the left is reproduced on all relevant spreads of this catalog.  
We are unique in conducting a QC test for supports to show the length of oligo that can be prepared before a drop-off incoupling due to steric effects begins to occur.  The drop-off point is recorded in the Certificate of Analysis or Analytical Report.  
Unless otherwise specified, our minor base and modification supports are 1000Å CPG, which results in improved performanceand the ability to make much longer oligos.  Polystyrene supports are also available for some of our most popular items.
For reasons of quality assurance, we do not transfer powders or oils from stock Applied Biosystems vials to vials for other
instruments.  Powders may be hygroscopic and electrostatic, making transfer difficult, and oils have to be dissolved andthe solvent evaporated.  For best performance, it is preferable for the customer to dissolve the product and immediatelytransfer the solution to the correct instrument vial.  Consequently, the product will be delivered in an industry-standard
septum-capped vial along with a clean dry vial for the appropriate instrument.
Glen Research will only guarantee products purchased through our official distributors. A complete listing of authorized
distributors can be found on our website at: https://www.glenresearch.com/international-distributors.

QUALITY AND PERFORMANCE ASSURED
Glen Research has developed and implemented a Quality Management System (QMS) designed to enhancecustomer satisfaction by focusing on processes for continual improvement and on assurance of conformity tocustomer needs, with full consideration of applicable regulatory requirements.   

STERLING QUALITY

STERLING PERFORMANCEThe benchmark for excellence in DNA andRNA   synthesis.   All Sterling materials must
pass stringent purity and identity tests prior toacceptance.   Sterling products are formulated,filtered, and packaged in optimal environments
using specially cleaned and dried glasswareand columns.   Color-coded labeling and postpackaging analysis guarantee accuracy andSterling Quality.

ence Since 1987
ExcellThe standard of accomplishment for DNA andRNA synthesis.  Every batch of Sterling reagents isanalyzed by titration to confirm exact formulation.  
Every batch of Sterling monomers, supports andactivators is synthesis-tested to ensure optimal
performance.  Certificates of Analysis provide yourguarantee of Sterling Performance.

   STERLING is a trademark of Glen Research Corporation.
Glen Research offers the highest level of Quality Assurance for reagents for DNA and RNA synthesis - Sterling
Quality and Performance.   We now apply the Sterling criteria of quality and performance to all of Glen Research’s
established products.

STERLING

The common monomers and supports, whose structures are illustrated below, are available for the variety ofsynthesizers listed on the following pages.
NHBz

NHBz
N

N

N

N

N

DMTO

O

DMTO

O

DMTO

N

dC-CE Phosphoramidite

NHBz

NHBz
N
DMTO

O

O

C CH 2CH 2 CO

dA-lcaa-CPG

O

lcaaCPGOOOC CH 2CH 2 COOdC-lcaa-CPG

O P N(iPr)2

O P N(iPr)2

dG-CE Phosphoramidite

dT-CE Phosphoramidite

lcaaCPG

iBuHN
DMTO

N
O

O

C CH 2CH 2 C
OOAc-dC-lcaa-CPG

lcaaCPG

O

N

HN

O

O CNEt

O

N
DMTO

N
O

O CNEt

NHAc

N

O

DMTO

O

O CNEt

Ac-dC-CE Phosphoramidite

DMTO

O

C CH 2CH 2 C

O

CH 3

HN

N

N

O

CH 3

HN

N

N

O P N(iPr)2

N

N

iBuHN
DMTO

N

O

N

HN

O

O CNEtdA-CE Phosphoramidite

N

O

DMTO

O P N(iPr)2

O CNEtONOO P N(iPr)2

N

NHAc

O

dG-lcaa-CPG

lcaaCPGNOOOC CH 2CH 2 COOdT-lcaa-CPG

7

lcaaCPGMISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLING

STERLINGAPPLIED BIOSYSTEMS INSTRUMENTS
STERLING CE PHOSPHORAMIDITESQUALITY ASSURANCE
Every batch of these CE
Phosphoramidites is tested as follows:
1. HPLCa) Identity is confirmed by comparison
with a reference sample.
b) Purity is determined by HPLC to be≥98.0%.
2. TLCPurity is verified by TLC.
3. 31P NMR
Purity is determined by 31P NMR tobe ≥98%.
4. Coupling Test
Coupling efficiency is determined tobe ≥99%.
5. Solution Test
A 0.1M solution is determined to
be clear and free of particulatecontamination.
6. Loss on Drying
Volatile contaminants are determined
to be ≤2%.

Glen Research CE (β-cyanoethyl) Phosphoramidites are produced and packaged to ensure the highest performance on DNA
synthesizers. Every Glen Research product is accompanied by a Certificate of Analysis and HPLC trace, showing the resultsof our QC testing. Every Glen Research monomer vial is specially cleaned to eliminate particulate contamination, and eachvial type is thoroughly tested or inspected to ensure a tight fit on synthesizers..

Item

Catalog No.

Pack

dA-CE Phosphoramidite

10-1000-02
10-1000-05
10-1000-10
10-1000-20
10-1000-40
10-1010-02
10-1010-05
10-1010-10
10-1010-20
10-1010-40
10-1015-02
10-1015-05
10-1015-10
10-1015-20
10-1015-40
10-1020-02
10-1020-05
10-1020-10
10-1020-20
10-1020-40
10-1029-02
10-1029-05
10-1029-10
10-1029-20
10-1029-40
10-1030-02
10-1030-05
10-1030-10
10-1030-20
10-1030-40

0.25g
0.5g
1.0g
2.0g
4.0g
0.25g
0.5g
1.0g
2.0g
4.0g
0.25g
0.5g
1.0g
2.0g
4.0g
0.25g
0.5g
1.0g
2.0g
4.0g
0.25g
0.5g
1.0g
2.0g
4.0g
0.25g
0.5g
1.0g
2.0g
4.0g

dC-CE Phosphoramidite

Ac-dC-CE Phosphoramidite

O
N

HN

(Me) 2N

N

N

N

DMTO

dG-CE PhosphoramiditeO
O P N(iPr)2

dmf-dG-CE Phosphoramidite

O CNEtdmf-dG-CE Phosphoramidite

ABI INSTRUMENTS
1. 60mL septum-capped vials usedon oldest ABI 380, 381 and 391
instruments.  200mL oxidizer and
450mL deblock screw-capped bottles
also used on ABI 380, 381 and 391
instruments.
2. Small screw-capped vials used on ABI
392 and 394 instruments.
3. Larger screw-capped vials used on
ABI 392. 394 and 3400 instruments.
4. Large bottles used on ABI 3900
instruments.

RELATED
Depurination Resistant dA.........26

dT-CE Phosphoramidite

STERLING SOLVENTS/REAGENTS
All solvents and reagents are prepared to our exacting specifications to ensure the highest synthesis efficiency and arepassed through a 0.2 micron filter during packaging to eliminate particulate contamination. Glen Research uses freshly
sublimed 1H-tetrazole for premium performance on Applied Biosystems synthesizers.

Item
Activator
Tetrazole in Acetonitrile

Diluent
Acetonitrile, anhydrous

8

Catalog No.

Pack

30-3100-451
30-3100-522
30-3100-573
30-3100-624

45mL
200mL
450mL
2000mL40-4050-45
40-4050-50

60mL
100mL

STERLING CE PHOSPHORAMIDITES (CONT.)
Item

Catalog No.

Cap Mix A
Tetrahydrofuran/Pyridine/Acetic Anhydride

Cap Mix B
16%  1-Methylimidazole in Tetrahydrofuran(This Cap B solution is identical to theformulation produced by Applied Biosystems.)
Oxidizing Solution
0.02M Iodine in Tetrahydrofuran/Pyridine/Water

Deblocking Mix
3% Trichloroacetic Acid/DichloromethanePack

40-4110-522
40-4110-573
40-4110-624

200mL
450mL
2000mL40-4220-522
40-4220-624

200mL
2000mL40-4330-521,240-4330-573
40-4330-624

200mL
450mL
2000mL40-4140-571,240-4140-623,4

450mL
2000mLSTERLING SUPPORTS
All Glen Research CPG supports use the standard long chain alkylamino (lcaa) linker but differ in the glass pore size, 500Å,
1000Å or 2000Å. The 500Å support is appropriate for shorter sequences, while the 1000Å supports perform better inthe synthesis of longer (>30-mer) DNA sequences. The 2000Å support is best for very long (>150-mer) oligonucleotides.
We have instituted an additional QC test for supports to show the length of oligo that can be prepared before a drop-off incoupling due to steric effects begins to occur. The drop-off point is recorded in the Certificate of Analysis. All Glen Researchsupports are fully end-capped to ensure that the CPG surface is totally inert, thereby avoiding the introduction of impurity
sequences containing deletions at the 3’-terminus.

Catalog No.
dA

Catalog No.
dC

Catalog No.
dG

Catalog No.
dT

Catalog No. Catalog No.
dA,dC,dG,dT
Ac-dC

Catalog No.
dmf-dGABBREVIATIONSAc2O = Acetic Anhydride
CE = Cyanoethyl
CPG = Controlled Pore Glass
DCM = Dichloromethane
dmf = dimethylformamidine
I2 = Iodine
lcaa = long chain alkylamino
MeIm = 1-Methylimidazoleµm = micromole(s)nm = nanomole(s)TCA = Trichloroacetic Acid
THF = Tetrahydrofuran

RELATED
Alternative Solvents...................34

O(Me) 2N

N

HN
N
DMTO

N

N
O
O C
O

dmf-dG-CPG

Pack(1 column of)each base)500Å Columns
20-2100-42
20-2100-41
20-2100-13

20-2110-42
20-2110-41
20-2110-13

20-2120-42
20-2120-41
20-2120-13

20-2130-42
20-2130-41
20-2130-13

20-2140-42
20-2140-41

20-2113-42
20-2113-41
20-2113-13

20-2111-45
20-2111-42
20-2111-41
20-2111-13

20-2121-45
20-2121-42
20-2121-41
20-2121-13

20-2131-45
20-2131-42
20-2131-41
20-2131-13

20-2141-45
20-2141-42
20-2141-41

20-2115-45
20-2115-42
20-2115-41
20-2115-13

4x0.2µm
4x1.0µm
1x10µm1000Å Columns
20-2101-45
20-2101-42
20-2101-41
20-2101-13

20-2129-45
20-2129-42
20-2129-41
20-2129-13

CH 2CH 2 C

4x40nm4x0.2µm
4x1.0µm
1x10µm9Olcaa CPGMISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGAPPLIED BIOSYSTEMS INSTRUMENTSAPPLIED BIOSYSTEMS INSTRUMENTS
STERLING SUPPORTS (CONT.)ABI 3900 1000Å CPG
COLUMNS
Glen Research’s ABI 3900 1000Å CPG
columns bring the lower cost of CPG
to this platform while maintaining thehigh synthesis efficiency of 1000Å CPG.  
Our columns offer the following key
attributes:• No need to change instrument settings• No need to change softwareparameters• Easier handling post -synthesis
compared to PS• High quality 1000Å CPG for optimal
synthesis results

BULK CPG LOADING
500Å supports
1000Å supports

35-50µmoles/g
25-40µmoles/g

Catalog No.
dA

Catalog No.
dC

Catalog No.
dG

Catalog No. Catalog No. Catalog No.
dT
dA,dC,dG,dT
Ac-dC

Catalog No.
dmf-dGPack(1 column of)each base)2000Å Columns
20-2102-42

20-2112-42

20-2122-42

20-2132-42

20-2142-42

4x0.2µm

26-2130-45
26-2130-42

26-2140-45
26-2140-42

4x40nm4x0.2µm

Low Volume (LV) Polystyrene Columns
26-2100-45
26-2100-42

26-2110-45
26-2110-42

26-2120-45
26-2120-42

ABI 3900 Polystyrene Columns
26-2600-65
26-2600-62

26-2610-65
26-2610-62

RELATEDABI 3900 1000Å CPG Columns

Universal Supports.....................28
Q-Supports.................................31
High Load Supports....................33

20-2101-65
20-2101-62
20-2101-61

26-2630-65
26-2630-62

20-2131-65
20-2131-62
20-2131-61

20-2115-65
20-2115-62
20-2115-61

20-2020-01
20-2020-02
20-2020-10

20-2030-01
20-2030-02
20-2030-10

20-2013-01
20-2013-02
20-2013-10

20-2021-01
20-2021-02
20-2021-10

20-2031-01
20-2031-02
20-2031-10

20-2015-01
20-2015-02
20-2015-10

20-2022-01
20-2022-02
20-2022-10

20-2032-01
20-2032-02
20-2032-10

26-2629-65
26-2629-62

200x40nm
200x200nm

20-2129-65
20-2129-62
20-2129-61

200x40nm
200x200nm
200x1.0µm500Å Bulk CPG
20-2000-01
20-2000-02
20-2000-10

20-2010-01
20-2010-02
20-2010-10

0.1g
0.25g
1.0g

1000Å Bulk CPG
20-2001-01
20-2001-02
20-2001-10

20-2011-01
20-2011-02
20-2011-10

20-2029-01
20-2029-02
20-2029-10

0.1g
0.25g
1.0g

2000Å Bulk CPG
20-2002-01
20-2002-02
20-2002-10

20-2012-01
20-2012-02
20-2012-10

Item

Catalog No.

Pack

Empty Synthesis Columns-TWIST 40nm, 0.2um or 1um
Empty Synthesis Columns - TWIST 10um/15um
Replacement Frits - TWIST 10um/15um

20-0030-00
20-0040-00
20-0040-0F

Pack of 10
Pack of 10
Pack of 20

TWIST is a trademark of Glen Research Corporation.

10

0.1g
0.25g
1.0g

ABI 3900 POLYSTYRENE MODIFIER COLUMNSRELATED

Some of our more popular minor base and modifier supports are available on polystyrene in columns fully compatible with
the Applied Biosystems 3900 synthesizer. These include our popular Universal Support III, which will allow DNA, RNA or LNA
oligos to be produced on the 3900 with ANY base at the 3’ terminus. At the same time, we are offering 1 μmole columnsof Universal Support III for the 3900 instrument. Structures and more complete descriptions are found in the relevant
catalog sections for each item. ABI 3900 columns can be prepared with virtually any of the CPG supports in this catalog.
It is no longer necessary to adjust the flow using our ABI 3900 CPG columns, as noted in the box to the right. Modified CPG
columns are only available in 200 nmole size - simple add ‘A’ to the regular catalog number to order.

Item		

Catalog No.

Pack

Universal Support III PS
200 nmole columns
   40 nmole columns (ABI 3900 Format)

26-5110-52
26-5110-55

Pack of 10
Pack of 10

Glen UnySupport™ PS
   200 nmole columns
   40 nmole columns

26-5140-52
26-5140-55

Pack of 10
Pack of 10

3’-Phosphate PS   200 nmole columns
   40 nmole columns

26-2900-52
26-2900-55

Pack of 10
Pack of 10

3’-PT-Amino-Modifier C6 PS
   200 nmole columns
   40 nmole columns

26-2956-52
26-2956-55

Pack of 10
Pack of 10

3’-(6-FAM) PS
   200 nmole columns
   40 nmole columns

26-2961-52
26-2961-55

Pack of 10
Pack of 10

3’-Dabcyl PS   200 nmole columns
   40 nmole columns

26-5912-52
26-5912-55

Pack of 10
Pack of 10

3’-TAMRA PS
   200 nmole columns
   40 nmole columns

26-5910-52
26-5910-55

Pack of 10
Pack of 10

3’-BiotinTEG PS
200 nmole columns
   40 nmole columns

26-2955-52
26-2955-55

Pack of 10
Pack of 10

Universal Supports.....................28

ABI 3900 1000Å CPG
COLUMNS
Glen Research’s ABI 3900 1000Å CPG
columns bring the lower cost of CPG
to this platform while maintaining thehigh synthesis efficiency of 1000Å CPG.  
Our columns offer the following key
attributes:• No need to change instrument settings• No need to change software parameters• Easier handling post -synthesis
compared to PS• High quality 1000Å CPG for optimal
synthesis results

11

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGAPPLIED BIOSYSTEMS INSTRUMENTS

EXPEDITE™ INSTRUMENTS
STERLING CE PHOSPHORAMIDITESQUALITY ASSURANCE
Every batch of these CE
Phosphoramidites is tested as follows:
1. HPLCa) Identity is confirmed by comparison
with a reference sample.
b) Purity is determined by HPLC to be≥98.0%.
2. TLC
Purity is verified by TLC.
3. 31P NMR
Purity is determined by 31P NMR tobe ≥98%.
4. Coupling Test
Coupling efficiency is determined tobe ≥99%.
5. Solution Test
A 0.1M solution is determined to
be clear and free of particulatecontamination.
6. Loss on Drying
Volatile contaminants are determined
to be ≤2%.

Glen Research CE (β-cyanoethyl) Phosphoramidites are produced and packaged to ensure the highest performance on
DNA synthesizers. Every Glen Research product is accompanied by a Certificate of Analysis and HPLC trace, showing theresults of our QC testing. Every Glen Research monomer vial is specially cleaned to eliminate particulate contamination.

Item

Catalog No.

Pack

dA-CE Phosphoramidite

10-1000-C2
10-1000-C5
10-1000-1C
10-1000-2C

0.25g
0.5g
1.0g
2.0g

dC-CE Phosphoramidite

10-1010-C2
10-1010-C5
10-1010-1C
10-1010-2C

0.25g
0.5g
1.0g
2.0g

Ac-dC-CE Phosphoramidite

10-1015-C2
10-1015-C5
10-1015-1C
10-1015-2C

0.25g
0.5g
1.0g
2.0g

dG-CE Phosphoramidite

10-1020-C2
10-1020-C5
10-1020-1C
10-1020-2C

0.25g
0.5g
1.0g
2.0g

dmf-dG-CE Phosphoramidite

10-1029-C2
10-1029-C5
10-1029-1C
10-1029-2C

0.25g
0.5g
1.0g
2.0g

dT-CE Phosphoramidite

10-1030-C2
10-1030-C5
10-1030-1C
10-1030-2C

0.25g
0.5g
1.0g
2.0g

RELATED
Depurination Resistant dA.........26

EXPEDITE INSTRUMENTS
1. For use on Expedite 8905
instruments.
2. For use on Expedite 8909
instruments.

STERLING SOLVENTS/REAGENTS
All solvents and reagents are prepared to our exacting specifications to ensure the highest synthesis efficiency and arepassed through a 0.2 micron filter during packaging to eliminate particulate contamination. Glen Research uses freshly
sublimed 1H-tetrazole for premium performance on Expedite synthesizers.

Item
Activator
Tetrazole in Acetonitrile

Diluent
Acetonitrile, anhydrous

12

Catalog No.

Pack

30-3102-661
30-3102-522
30-3100-572

60mL
200mL
450mL

40-4050-45
40-4050-50

60mL
100mL

STERLING SOLVENTS/REAGENTS (CONT.)
Item

Catalog No.

Anhydrous Wash
Acetonitrile, anhydrous
Cap Mix A
Tetrahydrofuran/Acetic Anhydride
Cap Mix B
10% 1-Methylimidazole in Tetrahydrofuran/Pyridine
Oxidizing Solution
0.02M Iodine in Tetrahydrofuran/Water/Pyridine
Deblocking Mix
3% Trichloroacetic Acid/DichloromethanePack

40-4050-531
40-4050-572

300mL
450mL

40-4012-522
40-4012-57

200mL
450mL

40-4122-522
40-4122-57

200mL
450mL

40-4132-522
40-4132-57

200mL
450mL

40-4140-712

1L

ABBREVIATIONSAc2O = Acetic Anhydride
CE = Cyanoethyl
CPG = Controlled Pore Glass
DCM = Dichloromethane
dmf = dimethylformamidine
I2 = Iodine
lcaa = long chain alkylamino
MeIm = 1-Methylimidazoleµm = micromole(s)nm = nanomole(s)TCA = Trichloroacetic Acid
THF = Tetrahydrofuran

RELATED
Alternative Solvents...................34

BULK CPG LOADINGSTERLING SUPPORTS

500Å supports
1000Å supports

All Glen Research supports use the standard long chain alkylamino (lcaa) linker but differ in the glass pore size, 500Å,
1000Å or 2000Å. The 500Å support is appropriate for shorter sequences, while the 1000Å supports perform better inthe synthesis of longer (>30-mer) DNA sequences. The 2000Å support is best for very long (>150-mer) oligonucleotides.
We have instituted an additional QC test for supports to show the length of oligo that can be prepared before a drop-off incoupling due to steric effects begins to occur. The drop-off point is recorded in the Certificate of Analysis. All Glen Researchsupports are fully end-capped to ensure that the CPG surface is totally inert, thereby avoiding the introduction of impurity
sequences containing deletions at the 3’-terminus.

Catalog No.
Catalog No.
Catalog No.
Catalog No.
dA
dC
dG
dT
					

Catalog No.
dA,dC,dG,dT(1 column ofeach base)

Catalog No.
Ac-dC

Catalog No.
dmf-dG

Pack

500Å Columns
20-2200-42
20-2200-41
20-2200-14

20-2210-42
20-2210-41
20-2210-14

20-2220-42
20-2220-41
20-2220-14

20-2230-42
20-2230-41
20-2230-14

20-2240-42
20-2240-41

20-2213-42
20-2213-41
20-2213-14

20-2211-45
20-2211-42
20-2211-41
20-2211-14

20-2221-45
20-2221-42
20-2221-41
20-2221-14

20-2231-45
20-2231-42
20-2231-41
20-2231-14

20-2241-45
20-2241-42
20-2241-41

20-2215-45
20-2215-42
20-2215-41
20-2215-14

4x0.2µm
4x1.0µm
1x15µm1000Å Columns
20-2201-45
20-2201-42
20-2201-41
20-2201-14

20-2229-45
20-2229-42
20-2229-41
20-2229-14

4x40nm4x0.2µm
4x1.0µm
1x15µm13

35-50µmoles/g
25-40µmoles/g

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLING

EXPEDITE™ INSTRUMENTS

EXPEDITE™ INSTRUMENTS
STERLING SUPPORTS (CONT.)
RELATED
Universal Supports.....................28
Q-Supports.................................31
High Load Supports....................33

Catalog No.
Catalog No.
Catalog No.
Catalog No.
dA
dC
dG
dT
					

Catalog No.
dA,dC,dG,dT(1 column ofeach base)

Catalog No.
Ac-dC

Catalog No.
dmf-dG

Pack

2000Å Columns
20-2202-42

20-2212-42

20-2222-42

20-2232-42

20-2242-42

4x0.2µm

20-2010-01
20-2010-02
20-2010-10

20-2020-01
20-2020-02
20-2020-10

20-2030-01
20-2030-02
20-2030-10

20-2013-01
20-2013-02
20-2013-10

20-2021-01
20-2021-02
20-2021-10

20-2031-01
20-2031-02
20-2031-10

20-2015-01
20-2015-02
20-2015-10

20-2022-01
20-2022-02
20-2022-10

20-2032-01
20-2032-02
20-2032-10500Å Bulk CPG
20-2000-01
20-2000-02
20-2000-10

0.1g
0.25g
1.0g

1000Å Bulk CPG
20-2001-01
20-2001-02
20-2001-10

20-2011-01
20-2011-02
20-2011-10

20-2029-01
20-2029-02
20-2029-10

0.1g
0.25g
1.0g

2000Å Bulk CPG
20-2002-01
20-2002-02
20-2002-10

20-2012-01
20-2012-02
20-2012-10

Item

Catalog No.

Pack

Empty Synthesis Columns, 40nm, 0.2um Expedite Style
Empty Synthesis Columns, 1um Expedite Style
Replacement Filters-Expedite

20-0021-02
20-0021-01
20-0021-0F

Pack of 10
Pack of 10
Pack of 20

Empty Synthesis Columns - TWIST 10um/15um
Replacement Frits - TWIST 10um/15um

20-0040-00
20-0040-0F

Pack of 10
Pack of 20

TWIST is a trademark of Glen Research Corporation.
Expedite is a trademark of Applied Biosystems.

14

0.1g
0.25g
1.0g

DNA PHOSPHORAMIDITES - SPECIAL PACKAGING
We offer our high quality DNA phosphoramidites specifically packaged for high throughput and large-scale synthesis
customers. These customers normally require high quality materials produced under the guidelines of a validated quality
management system while still being priced aggressively. These products include the usual Glen Research certification andguarantees and they are available in larger packs or in bulk. The core catalog numbers for regular DNA phosphoramidites
are shown below. For these products, please request a quote.

Item

Catalog No.

dA-CE Phosphoramidite
dC-CE Phosphoramidite
Ac-dC-CE Phosphoramidite
dG-CE Phosphoramidite
dmf-dG-CE Phosphoramidite
dT-CE Phosphoramidite

10-1000-SP
10-1010-SP
10-1015-SP
10-1020-SP
10-1029-SP
10-1030-SP

INSTRUMENT TYPES
Glen Research packages thesemonomers in a variety of industrystandard vials and bottles.  Pleaseprovide the exact specification of thebottle required prior to receiving aquotation.

15

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGDNA PHOSPHORAMIDITES - SPECIAL PACKAGINGMERMADE INSTRUMENTS
STERLING CE PHOSPHORAMIDITESQUALITY ASSURANCE
Every batch of these CE
Phosphoramidites is tested as follows:
1. HPLCa) Identity is confirmed by comparison
with a reference sample.
b) Purity is determined by HPLC to be≥98.0%.
2. TLC
Purity is verified by TLC.
3. 31P NMR
Purity is determined by 31P NMR tobe ≥98%.
4. Coupling Test
Coupling efficiency is determined tobe ≥99%.
5. Solution Test
A 0.1M solution is determined to
be clear and free of particulatecontamination.
6. Loss on Drying
Volatile contaminants are determined
to be ≤2%.

MerMade synthesizers belong to a family of synthesizers, including the column-based MerMade 4, MerMade 6 and 12
instruments and the parallel array synthesizers, MerMade 192 and MerMade 192E, manufactured by BioAutomation
Corporation. Their website can be found at: http://www.BioAutomation.com. Phosphoramidite monomers are packaged in
30mL and 240mL amber bottles for dissolving at a concentration of 1g/20mL and are connected directly to the instrument.
Some instruments may also be configured to accept Applied Biosystems serum vials, as shown on page 6.

Item

Catalog No.

Pack

dA-CE Phosphoramidite

10-1000-02M
10-1000-05M
10-1000-10M
10-1000-5S
10-1000-1S
10-1010-02M
10-1010-05M
10-1010-10M
10-1010-5S
10-1010-1S
10-1015-02M
10-1015-05M
10-1015-10M
10-1015-5S
10-1015-1S
10-1020-02M
10-1020-05M
10-1020-10M
10-1020-5S
10-1020-1S
10-1029-02M
10-1029-05M
10-1029-10M
10-1029-5S
10-1029-1S
10-1030-02M
10-1030-05M
10-1030-10M
10-1030-5S
10-1030-1S

0.25g
0.5g
1.0g
5.0g
10.0g
0.25g
0.5g
1.0g
5.0g
10.0g
0.25g
0.5g
1.0g
5.0g
10.0g
0.25g
0.5g
1.0g
5.0g
10.0g
0.25g
0.5g
1.0g
5.0g
10.0g
0.25g
0.5g
1.0g
5.0g
10.0g

dC-CE Phosphoramidite

Ac-dC-CE Phosphoramidite
RELATED
Depurination Resistant dA.........26
Alternative Activators................34

dG-CE Phosphoramidite

dmf-dG-CE Phosphoramidite

dT-CE Phosphoramidite

STERLING SOLVENTS/REAGENTS
All solvents and reagents are prepared to our exacting specifications to ensure the highest synthesis efficiency and arepassed through a 0.2 micron filter during packaging to eliminate particulate contamination. Parallel synthesizers typicallyuse 5-ethylthio-1H-tetrazole (ETT) as activator to minimize the chance of crystallization. ETT is used at a concentration of
0.25M in acetonitrile, which is far below the level at which crystallization may occur.

Item
Activator
0.25M 5-Ethylthio-1H-Tetrazole in Acetonitrile

16

Catalog No.

Pack

30-3140-57
30-3140-61
30-3140-62

450mL
960mL
2000mLSTERLING SOLVENTS/REAGENTS (CONT.)
Item

Catalog No.

Diluent
Acetonitrile, anhydrous
Cap Mix A
THF/2,6-Lutidine/Acetic Anhydride

Cap Mix B
16%  1-Methylimidazole in Tetrahydrofuran

Ozidizing Solution
0.02M Iodine in Tetrahydrofuran/Pyridine/Water

Deblocking Mix
3% Dichloroacetic acid in Dichloromethane

3% Trichloroacetic Acid/DichloromethanePack

40-4050-50

100mL

40-4010-57
40-4010-61
40-4010-62

450mL
960mL
2000mL40-4220-57
40-4220-61
40-4220-62

450mL
960mL
2000mL40-4330-57
40-4330-61
40-4330-62

450mL
960mL
2000mL40-4040-57
40-4040-61
40-4040-62
40-4140-57
40-4140-61
40-4140-62

450mL
960mL
2000mL
450mL
960mL
2000mLABBREVIATIONSAc2O = Acetic Anhydride
CE = Cyanoethyl
CPG = Controlled Pore Glass
DCM = Dichloromethane
dmf = dimethylformamidine
I2 = Iodine
MeIm = 1-Methylimidazole
TCA = Trichloroacetic Acid
THF = Tetrahydrofuran

RELATED
Alternative Solvents...................34
Universal Supports.....................28
Q-Supports.................................31
High Load Supports....................33

STERLING SUPPORTS
Columns containing 1000Å CPG are available in packs of 200 to fit MerMade plates. Regular 500Å or 1000Å supports may
also be used to fill the wells of regular 96 well plates. However, this requires each plate to be prepared with each nucleosideaccurately in all wells. A universal support clearly removes the need for four specific supports and makes preparing plates
straightforward. Glen UnySupport™ 40 nmole frits can also be used.

Catalog No.
Catalog No.
dA
dC
Mermade 1000Å Columns
20-2001-65
20-2001-62
20-2001-61

Catalog No.
dG

Catalog No.
dT

Catalog No.
Ac-dC

Catalog No.		
dmf-dG

20-2021-65
20-2021-62
20-2021-61

20-2031-65
20-2031-62
20-2031-61

20-2015-65
20-2015-62
20-2015-61

20-2029-65
20-2029-62
20-2029-61

Item
Glen UnySupport™ 1000
1 µmole columns
   200 nmole columns
   40 nmole columns
Empty MerMade Columns
Empty MerMade Columns (50nm)
Empty MerMade Columns (200nm and 1µm)

Pack

200x50nm
200x200nm
48x1.0µm

Catalog No.

Pack

20-5141-91
20-5141-92
20-5141-95

Pack of 96
Pack of 96
Pack of 96

20-0050-05
20-0050-02

Pack of 48
Pack of 48

17

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGMERMADE INSTRUMENTSÄKTA OLIGOPILOT
STERLING CE PHOSPHORAMIDITESQUALITY ASSURANCE
Every batch of these CE
Phosphoramidites is tested as follows:
1. HPLCa) Identity is confirmed by comparison
with a reference sample.
b) Purity is determined by HPLC to be≥98.0%.
2. TLC
Purity is verified by TLC.
3. 31P NMR
Purity is determined by 31P NMR tobe ≥98%.
4. Coupling Test
Coupling efficiency is determined tobe ≥99%.
5. Solution Test
A 0.1M solution is determined to
be clear and free of particulatecontamination.
6. Loss on Drying
Volatile contaminants are determined
to be ≤2%.

RELATED

Glen Research CE (β-cyanoethyl) Phosphoramidites are produced and packaged to ensure the highest performance on
DNA synthesizers. Every Glen Research product is accompanied by a Certificate of Analysis and HPLC trace, showing theresults of our QC testing. Every Glen Research monomer vial is specially cleaned to eliminate particulate contamination.

Item

Catalog No.

Pack

dA-CE Phosphoramidite

10-1000-20
10-1000-50

2.0g
5.0g

dC-CE Phosphoramidite

10-1010-20
10-1010-50

2.0g
5.0g

Ac-dC-CE Phosphoramidite

10-1015-20
10-1015-50

2.0g
5.0g

dG-CE Phosphoramidite

10-1020-20
10-1020-50

2.0g
5.0g

dmf-dG-CE Phosphoramidite

10-1029-20
10-1029-50

2.0g
5.0g

dT-CE Phosphoramidite

10-1030-20
10-1030-50

2.0g
5.0g

Depurination Resistant dA.........26

18

STERLING SOLVENTS/REAGENTS
All solvents and reagents are prepared to our exacting specifications to ensure the highest synthesis efficiency and arepassed through a 0.2 micron filter during packaging to eliminate particulate contamination.

Item

Catalog No.

Pack

40-4050-45
40-4050-50

60mL
100mL

Activator
0.40M Tetrazole in Acetonitrile

30-3105-71

1L

Cap Mix A
Acetonitrile/1-Methylimidazole
20% 1-Methylimidazole in Acetonitrile/ 2,6-Lutidine

40-4015-71
40-4115-71

1L
1L

Cap Mix B
Acetonitrile/Acetic Anhydride/2,6-Lutidine*
20% Acetic Anhydride in Acetonitrile
5% Phenoxyacetic Anhydride in Acetonitrile

40-4028-71
40-4224-71
40-4128-71

1L
1L
1L

Oxidizing Solution
0.05M Iodine in Pyridine/Water

40-4035-71

1L

Deblocking Mix
3% Dichloroacetic Acid in Dichloromethane
3% Trichloroacetic Acid in Dichloromethane
3% Dichloroacetic Acid in Toluene

40-4040-71
40-4140-71
40-4240-71

1L
1L
1L

Diluent
Acetonitrile, anhydrous

ABBREVIATIONSAc2O = Acetic Anhydride
CE = Cyanoethyl
CPG = Controlled Pore Glass
DCA = Dichloroacetic Acid
DCM = Dichloromethane
I2 = Iodine
MeIm = 1-Methylimidazoleµm = micromole(s)RELATED
Alternative Solvents...................34*Cap Mix B is a two part
formulation that is combined
immediately before shipment.

19

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGÄKTA OLIGOPILOT

DR. OLIGO INSTRUMENTS
STERLING CE PHOSPHORAMIDITESQUALITY ASSURANCE
Every batch of these CE
Phosphoramidites is tested as follows:
1. HPLCa) Identity is confirmed by comparison
with a reference sample.
b) Purity is determined by HPLC to be≥98.0%.
2. TLC
Purity is verified by TLC.
3. 31P NMR
Purity is determined by 31P NMR tobe ≥98%.
4. Coupling Test
Coupling efficiency is determined tobe ≥99%.
5. Solution Test
A 0.1M solution is determined to
be clear and free of particulatecontamination.
6. Loss on Drying
Volatile contaminants are determined
to be ≤2%.

RELATED

Dr. Oligo synthesizers belong to a family of synthesizers, including the parallel array synthesizers, Dr. Oligo 96, Dr. Oligo
192, Dr. Oligo 384 and Dr. Oligo 768, manufactured by Biolytic® Lab Performance, Inc. in Fremont, CA. Their web site canbe found at: http://www.biolytic.com. Phosphoramidite monomers are packaged in 30mL and 240mL amber bottles fordissolving at a concentration of 1g/20mL and are connected directly to the instrument. Some instruments may also be
configured to accept Applied Biosystems serum vials.

Item

Catalog No.

Pack

dA-CE Phosphoramidite

10-1000-02M
10-1000-05M
10-1000-10M
10-1000-5S
10-1000-1S

0.25g
0.5g
1.0g
5.0g
10.0g

dC-CE Phosphoramidite

10-1010-02M
10-1010-05M
10-1010-10M
10-1010-5S
10-1010-1S

0.25g
0.5g
1.0g
5.0g
10.0g

Ac-dC-CE Phosphoramidite

10-1015-02M
10-1015-05M
10-1015-10M
10-1015-5S
10-1015-1S

0.25g
0.5g
1.0g
5.0g
10.0g

dG-CE Phosphoramidite

10-1020-02M
10-1020-05M
10-1020-10M
10-1020-5S
10-1020-1S

0.25g
0.5g
1.0g
5.0g
10.0g

dmf-dG-CE Phosphoramidite

10-1029-02M
10-1029-05M
10-1029-10M
10-1029-5S
10-1029-1S

0.25g
0.5g
1.0g
5.0g
10.0g

dT-CE Phosphoramidite

10-1030-02M
10-1030-05M
10-1030-10M
10-1030-5S
10-1030-1S

0.25g
0.5g
1.0g
5.0g
10.0g

Depurination Resistant dA.........26
Alternative Activators................34

STERLING SOLVENTS/REAGENTS
All solvents and reagents are prepared to our exacting specifications to ensure the highest synthesis efficiency and arepassed through a 0.2 micron filter during packaging to eliminate particulate contamination. Parallel synthesizers typicallyuse 5-ethylthio-1H-tetrazole (ETT) as activator to minimize the chance of crystallization. ETT is used at a concentration of
0.25M in acetonitrile, which is far below the level at which crystallization may occur.
Item

20

Activator
0.25M 5-Ethylthio-1H-Tetrazole in Acetonitrile

Catalog No.

Pack

30-3140-57
30-3140-62

450mL
2000mLSTERLING SOLVENTS/REAGENTS (CONT.)
Item

Catalog No.

Diluent
Acetonitrile, anhydrous
Cap Mix A
Tetrahydrofuran/2,6-Lutidine/Acetic Anhydride

Cap Mix B
16% 1-Methylimidazole in Tetrahydrofuran

Oxidizing Solution
0.02M Iodine in Tetrahydrofuran/Pyridine/H2O

Deblocking Mix
3% Dichloroacetic acid in Dichloromethane
3% Trichloroacetic acid in DichloromethanePack

40-4050-50

100mL

40-4010-57
40-4010-62

450mL
2000mL40-4220-57
40-4220-62

450mL
2000mL40-4330-57
40-4330-62

450mL
2000mL40-4040-57
40-4040-62
40-4140-57
40-4140-62

450mL
2000mL
450mL
2000mLABBREVIATIONSAc2O = Acetic Anhydride
CE = Cyanoethyl
CPG = Controlled Pore Glass
DCM = Dichloromethane
dmf = dimethylformamidine
I2 = Iodine
MeIm = 1-Methylimidazole
TCA = Trichloroacetic Acid
THF = Tetrahydrofuran

RELATED
Alternative Solvents...................34
Universal Supports.....................28
Q-Supports.................................31
High Load Supports....................33
Glen-Pak™ DNA........................153

STERLING SUPPORTS
Dr. Oligo instruments are designed for flexibility in the use of supports and columns. They can use fritted plates withloose CPG and ABI 3900 style polystyrene and CPG columns. Glen UnySupport™ 40 nmole frits can also be used.
Catalog No.
dA

Catalog No.
dC

Catalog No.
dG

Catalog No.
dT

ABI 3900 Polystyrene Columns
26-2600-65
26-2610-65
26-2600-62
26-2610-62

26-2630-65
26-2630-62

ABI 3900 1000Å CPG Columns
20-2101-65
20-2101-62
20-2101-61

20-2131-65
20-2131-62
20-2131-61

Catalog No.
Ac-dC

20-2115-65
20-2115-62
20-2115-61

Catalog No.		
dmf-dG

Pack

26-2629-65
26-2629-62

200x40nm
200x200nm

20-2129-65
20-2129-62
20-2129-61

200x40nm
200x200nm
200x1.0µm

OLIGONUCLEOTIDE PURIFICATION
Biolytic Labs also offers the innovative Dr. Oligo Processor for high throughput purification of oligonucleotides using GlenPak™ DNA Purification Cartridges: https://www.biolytic.com/p-6814-dr-oligo-processor-fully-automated.aspx.

21

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLING

DR. OLIGO INSTRUMENTS

K & A INSTRUMENTS
STERLING CE PHOSPHORAMIDITESQUALITY ASSURANCE
Every batch of these CE
Phosphoramidites is tested as follows:
1. HPLCa) Identity is confirmed by comparison
with a reference sample.
b) Purity is determined by HPLC to be≥98.0%.
2. TLC
Purity is verified by TLC.
3. 31P NMR
Purity is determined by 31P NMR tobe ≥98%.
4. Coupling Test
Coupling efficiency is determined tobe ≥99%.
5. Solution Test
A 0.1M solution is determined to
be clear and free of particulatecontamination.
6. Loss on Drying
Volatile contaminants are determined
to be ≤2%.

RELATED

Glen Research CE (β-cyanoethyl) Phosphoramidites are produced and packaged to ensure the highest performance on
DNA synthesizers. Every Glen Research product is accompanied by a Certificate of Analysis and HPLC trace, showing theresults of our QC testing. Every Glen Research monomer vial is specially cleaned to eliminate particulate contamination.

Item

Catalog No.

Pack

dA-CE Phosphoramidite

10-1000-C2
10-1000-C5
10-1000-1C
10-1000-2C
10-1000-5S
10-1000-1S

0.25g
0.5g
1.0g
2.0g
5.0g
10.0g

dC-CE Phosphoramidite

10-1010-C2
10-1010-C5
10-1010-1C
10-1010-2C
10-1010-5S
10-1010-1S

0.25g
0.5g
1.0g
2.0g
5.0g
10.0g

Ac-dC-CE Phosphoramidite

10-1015-C2
10-1015-C5
10-1015-1C
10-1015-2C
10-1015-5S
10-1015-1S

0.25g
0.5g
1.0g
2.0g
5.0g
10.0g

dG-CE Phosphoramidite

10-1020-C2
10-1020-C5
10-1020-1C
10-1020-2C
10-1020-5S
10-1020-1S

0.25g
0.5g
1.0g
2.0g
5.0g
10.0g

dmf-dG-CE Phosphoramidite

10-1029-C2
10-1029-C5
10-1029-1C
10-1029-2C
10-1029-5S
10-1029-1S

0.25g
0.5g
1.0g
2.0g
5.0g
10.0g

dT-CE Phosphoramidite

10-1030-C2
10-1030-C5
10-1030-1C
10-1030-2C
10-1030-5S
10-1030-1S

0.25g
0.5g
1.0g
2.0g
5.0g
10.0g

Depurination Resistant dA.........26

EXPEDITE INSTRUMENTS
1. For use on Expedite 8905
instruments.
2. For use on Expedite 8909
instruments.

22

STERLING SOLVENTS/REAGENTS

ABBREVIATIONSAll solvents and reagents are prepared to our exacting specifications to ensure the highest synthesis efficiency and arepassed through a 0.2 micron filter during packaging to eliminate particulate contamination. Glen Research uses freshly
sublimed 1H-tetrazole for premium performance on Expedite synthesizers.

Item
Activator
Tetrazole in Acetonitrile

Diluent
Acetonitrile, anhydrous
Cap Mix A
Tetrahydrofuran/Acetic Anhydride

Cap Mix B
10% 1-Methylimidazole in Tetrahydrofuran/Pyridine

Oxidizing Solution
0.02M Iodine in Tetrahydrofuran/Water/Pyridine

Deblocking Mix
3% Trichloroacetic Acid/Dichloromethane

Catalog No.

Pack

30-3102-52
30-3100-57
30-3100-62

200mL
450mL
2000mL40-4050-50

100mL

40-4012-52
40-4012-57
40-4012-62

200mL
450mL
2000mL40-4122-52
40-4122-57
40-4122-62

200mL
450mL
2000mL40-4132-52
40-4132-57
40-4132-62

200mL
450mL
2000mL40-4140-62

2000mLAc2O = Acetic Anhydride
CE = Cyanoethyl
CPG = Controlled Pore Glass
DCM = Dichloromethane
dmf = dimethylformamidine
I2 = Iodine
lcaa = long chain alkylamino
MeIm = 1-Methylimidazoleµm = micromole(s)nm = nanomole(s)TCA = Trichloroacetic Acid
THF = Tetrahydrofuran

RELATED
Alternative Solvents...................34

BULK CPG LOADING
500Å supports
1000Å supports

2335-50µmoles/g
25-40µmoles/g

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLING

K & A INSTRUMENTS

K & A INSTRUMENTS
STERLING SUPPORTS
RELATED
Universal Supports.....................28
Q-Supports.................................31
High Load Supports....................33

All Glen Research supports use the standard long chain alkylamino (lcaa) linker but differ in the glass pore size, 500Å,
1000Å or 2000Å. The 500Å support is appropriate for shorter sequences, while the 1000Å supports perform better inthe synthesis of longer (>30-mer) DNA sequences. The 2000Å support is best for very long (>150-mer) oligonucleotides.
We have instituted an additional QC test for supports to show the length of oligo that can be prepared before a drop-off incoupling due to steric effects begins to occur. The drop-off point is recorded in the Certificate of Analysis. All Glen Researchsupports are fully end-capped to ensure that the CPG surface is totally inert, thereby avoiding the introduction of impurity
sequences containing deletions at the 3’-terminus.

Catalog No.
Catalog No.
Catalog No.
Catalog No.
dA
dC
dG
dT
					

Catalog No.
dA,dC,dG,dT(1 column ofeach base)

Catalog No.
Ac-dC

Catalog No.
dmf-dG

Pack

500Å Columns
20-2200-42
20-2200-41
20-2200-14

20-2210-42
20-2210-41
20-2210-14

20-2220-42
20-2220-41
20-2220-14

20-2230-42
20-2230-41
20-2230-14

20-2240-42
20-2240-41

20-2213-42
20-2213-41
20-2213-14

20-2211-45
20-2211-42
20-2211-41
20-2211-14

20-2221-45
20-2221-42
20-2221-41
20-2221-14

20-2231-45
20-2231-42
20-2231-41
20-2231-14

20-2241-45
20-2241-42
20-2241-41

20-2215-45
20-2215-42
20-2215-41
20-2215-14

20-2212-42

20-2222-42

20-2232-42

20-2242-42

20-2010-01
20-2010-02
20-2010-10

20-2020-01
20-2020-02
20-2020-10

20-2030-01
20-2030-02
20-2030-10

20-2013-01
20-2013-02
20-2013-10

20-2021-01
20-2021-02
20-2021-10

20-2031-01
20-2031-02
20-2031-10

20-2015-01
20-2015-02
20-2015-10

20-2022-01
20-2022-02
20-2022-10

20-2032-01
20-2032-02
20-2032-10

4x0.2µm
4x1.0µm
1x15µm1000Å Columns
20-2201-45
20-2201-42
20-2201-41
20-2201-14

20-2229-45
20-2229-42
20-2229-41
20-2229-14

4x40nm4x0.2µm
4x1.0µm
1x15µm2000Å Columns
20-2202-42

4x0.2µm500Å Bulk CPG
20-2000-01
20-2000-02
20-2000-10

0.1g
0.25g
1.0g

1000Å Bulk CPG
20-2001-01
20-2001-02
20-2001-10

20-2011-01
20-2011-02
20-2011-10

20-2029-01
20-2029-02
20-2029-10

0.1g
0.25g
1.0g

2000Å Bulk CPG
20-2002-01
20-2002-02
20-2002-10

24

20-2012-01
20-2012-02
20-2012-10

0.1g
0.25g
1.0g

MISCELLANEOUS

NOTES

25

ALTERNATIVE PROTECTING GROUPSDEPURINATION RESISTANT CE PHOSPHORAMIDITESOTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)
N(Et)2

N

N

N

N

N
DMTO

O
O

P

N(iPr)2O

CNEt

def-dA

Me

N

N

N

N
O
O

P

N(iPr)2

O

CNEt

dma-dAO(Me) 2N

N

HN
N
DMTO

The most commonly used dA-CE Phosphoramidite containing benzoyl protecting groups suffers substantial degradation
by depurination after excessive exposure to TCA.  At the same time, two depurination resistant dA monomers, protectedwith diethylformamidine (def) and dimethylacetamidine (dma), are essentially stable to depurination during the same
exposure to TCA.  
Both new depurination resistant dA monomers (def and dma protected), were rapidly deprotected in ammonium hydroxide
and are fully compatible with regular deprotection strategies.  Def-protected-dA was rapidly deprotected with AMA at 65°
in 20 minutes, which makes it fully compatible with regular AMA deprotection.  In contrast, the  dma-protected-dA required
80 minutes with AMA at 65° for complete deprotection.  
Dmf-dG is also a depurination resistant CE Phosphoramidite with the isobutyryl group of the original monomer replacedwith dimethylformamidine (dmf).
Although depurination does occur in regular oligonucleotide synthesis, the degradation is at an extremely low level.  
However in certain other circumstances, depurination may become more significant, such as synthesis of long oligos, chipbased synthesis, and large-scale synthesis.

Item

Catalog No.

Pack

def-dA-CE Phosphoramidite

10-1504-02
10-1504-05
10-1504-10

0.25g
0.5g
1.0g

dmf-dG-CE Phosphoramidite

10-1029-02
10-1029-05
10-1029-10
10-1029-20
10-1029-40

0.25g
0.5g
1.0g
2.0g
4.0g

N(Me)2N

DMTO

Depurination is defined as the cleavage of the glycosidic bond attaching a purine base to the sugar moiety.  
Electron withdrawing acyl protecting groups like benzoyl and isobutyryl on the purine amino group(s) destabilize theglycosidic bond, whereas electron donating formamidine protecting groups stabilize the glycosidic bond.  The consequenceof depurination during oligonucleotide synthesis is the loss of the purine base to form an internucleotide linkage containing
the abasic sugar at that position. This site is stable during further synthesis cycles but, upon deprotection with basic reagents,
the oligonucleotide is cleaved at that position leading to two shorter fragments. The fragment towards the 5’ terminus stillcontains the DMT group. If DMT-ON purification is being used, the depurinated fragments are co-purified along with thefull length product as truncated oligonucleotides.

NNO

O P N(iPr)2
O CNEtdmf-dG

26

ULTRAMILD CE PHOSPHORAMIDITESAn alternative protecting scheme for the normal CE phosphoramidites should allow UltraMILD deprotection and should notreact with a wider variety of tags and labels.  A set of monomers using phenoxyacetyl (Pac) protected dA and 4-isopropylphenoxyacetyl (iPr-Pac) protected dG, along with acetyl protected dC, met the desired criteria for UltraMILD deprotection.
We recommend the use of phenoxyacetic anhydride (Pac2O) in Cap A,which removes the possibility of exchange of the iPr-Pac
protecting group on the dG with acetate from the acetic anhydride capping mix.  Cleavage and deprotection can be carriedout in 2 hours at room temperature with ammonium hydroxide or 4 hours with 0.05M potassium carbonate in methanol.

Item

Catalog No.

Pack

Pac-dA-CE Phosphoramidite

10-1601-02
10-1601-05
10-1601-10

0.25g
0.5g
1.0g

10-1015-02
10-1015-05
10-1015-10

0.25g
0.5g
1.0g

10-1621-02
10-1621-05
10-1621-10

0.25g
0.5g
1.0g

Ac-dC-CE Phosphoramidite

iPr-Pac-dG-CE Phosphoramidite

ULTRAMILD SUPPORTS
Item				Catalog No.
Pac-dA

Catalog No.
Ac-dC

Catalog No.		
iPr-Pac-dG        UltraMild CPG (Bulk)

20-2601-01
20-2601-02
20-2601-10
20-2701-45
20-2701-42
20-2701-41
20-2701-13
20-2801-45
20-2801-42
20-2801-41
20-2801-14

ListedonPage 820-2115-45
20-2115-42
20-2115-41
20-2115-13
20-2215-45
20-2215-42
20-2215-41
20-2215-14

20-2621-01
20-2621-02
20-2621-10
20-2721-45
20-2721-42
20-2721-41
20-2721-13
20-2821-45
20-2821-42
20-2821-41
20-2821-14

ABI Columns

Expedite Columns

Cap Mix A
THF/Pyridine/Pac2O  
(Applied Biosystems)		
THF/Pac2O   
(Expedite)
Deprotection Solution
0.05M Potassium Carbonate in Methanol

Universal Support III...................30

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

Pack
0.1g
0.25g
1.0g
4X40nm
4X0.2µm
4X1µm
10µm
4X40nm
4X0.2µm
4X1µm
15µm

NHAc

NHAcOPh
N

N
DMTO

N

N

N

O

DMTO

O

O P N(iPr)2

O P N(iPr)2

O CNEtO CNEtPac-dA

Ac-dC

O

iPrPhOAcHN

Catalog No.

Pack

N
O

N

HN

ULTRAMILD SOLVENTS/REAGENTS
Item

RELATED

N

N

DMTO

O
O P N(iPr)240-4210-52
40-4210-57

200mL
450mL

40-4212-52
40-4212-57

200mL
450mL

60-4600-30
60-4600-52
60-4600-57

30mL
200mL
450mL

O CNEt

iPr-Pac-dG

27

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGULTRAMILD DNA SYNTHESISSUPPORTS
GLEN UNYSUPPORTOTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeEA
M

A recent development has been the use of a support based on a molecule which is “conformationally preorganized” toaccelerate the dephosphorylation reaction.1,2  By using a rigid bicyclic molecule on the support, the rate of elimination ismarkedly faster than the original Universal Support.  The structure of Glen UnySupport™ is shown below.  The N-phenyl
version, developed at Isis Pharmaceuticals as UnyLinker™, is available from several companies for large scale oligo synthesis.  
Glen UnySupport is the N-methyl version, which is preferred for high throughput oligonucleotide synthesis since methylamine
rather than aniline is formed on deprotection.  We are happy to offer Glen UnySupport in a variety of popular formats
under license from Ionis Pharmaceuticals.

Item
Bulk Supports
Glen UnySupport(500Å CPG)

Catalog No.

Pack

20-5040-01
20-5040-02
20-5040-10

0.1g
0.25g
1.0g

(Please inquire for availability of vials andcolumns for other instrument types.)

Glen UnySupport(1000Å CPG)

20-5041-01
20-5041-02
20-5041-10

0.1g
0.25g
1.0g

REFERENCES

Glen UnySupport(1400Å CPG)

20-5044-01
20-5044-02
20-5044-10

0.1g
0.25g
1.0g

Glen UnySupport(2000Å CPG)

20-5042-01
20-5042-02
20-5042-10

0.1g
0.25g
1.0g

High Load Glen UnySupport

25-5040-01
25-5040-02
25-5040-10

0.1g
0.25g
1.0g

Glen UnySupport PS

26-5040-01
26-5040-02
26-5040-10

0.1g
0.25g
1.0g

(1) A.P. Guzaev, and M. Manoharan, J Am
Chem Soc, 2003, 125, 2380-2381.
(2) R.K. Kumar, A.P. Guzaev, C. Rentel, and
V.T. Ravikumar, Tetrahedron, 2006, 62,
4528.

ELIMINATION CONDITIONSReagent

Conditions

Ammonium hydroxide

80°C/2h55°C/8h

Ammonium hydroxide/
40% Methylamine (AMA)

80°C/0.5h
65°C/1h55°C/8h

Methylamine Gas

65°C/0.5h/30psi

Potassium Carbonate
in Methanol

RT/17ht-Butylamine/Water (1:3 v/v)

60°C/4h

INTELLECTUAL PROPERTYThis product is covered by US
Patent 7,202,264 owned by Ionis
Pharmaceuticals, Inc..

O
Me N

O

ODMT

O

O
O

O

Glen UnySupport

28

N
H

Item
Columns1000Å
ABI Format (not LV)
1 µmole columns
0.2 µmole columns
40 nmole columns
10 µmole column (TWIST Format)

Catalog No.

20-5141-41
20-5141-42
20-5141-45
20-5141-13

Pack

Pack of 4
Pack of 4
Pack of 4
Pack of 1

26-5140-52
26-5140-55

Pack of 10
Pack of 10

Expedite Format
1 µmole columns
0.2 µmole columns
40 nmole columns
15 µmole column (TWIST Format)

20-5241-41
20-5241-42
20-5241-45
20-5241-14

Pack of 4
Pack of 4
Pack of 4
Pack of 1

96 Well Format (MerMade, etc.)
1 µmole columns
200 nmole columns
40 nmole columns

20-5141-91
20-5141-92
20-5141-95

Pack of 96
Pack of 96
Pack of 96

2000Å
ABI Format
0.2 µmole columns
Expedite Format
0.2 µmole columns

Reagent

Conditions

Ammonium hydroxide

80°C/2h55°C/8h

Ammonium hydroxide/
40% Methylamine (AMA)

80°C/0.5h
65°C/1h55°C/8h

Methylamine Gas

ABI 3900 Format
Glen UnySupport PS
200 nmole columns
40 nmole columns

1400Å
ABI Format
1 µmole columns
0.2 µmole columns
   10 µmole column (TWIST Format)
Expedite Format
1 µmole columns
0.2 µmole columns

ELIMINATION CONDITIONS

65°C/0.5h/30psi

Potassium Carbonate
in Methanol

RT/17ht-Butylamine/Water (1:3 v/v)

60°C/4h

INTELLECTUAL PROPERTYThis product is covered by US
Patent 7,202,264 owned by Ionis
Pharmaceuticals, Inc..

O
Me N

O

ODMT
O

O

H
N

O
O

O

Glen UnySupport FC

20-5144-41
20-5144-42
20-5144-13

Pack of 4
Pack of 4
Pack of 1

20-5244-41
20-5244-42

Pack of 4
Pack of 4

20-5142-42

Pack of 4

20-5242-42

Pack of 4

Please inquire about 500Å columns.

29

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGSUPPORTSSUPPORTS
UNIVERSAL SUPPORT III

REFERENCES(1) A.V. Azhayev, Tetrahedron, 1999, 55,
787-800.
(2) A.V. Azhayev and M. Antopolsky,
Tetrahedron, 2001, 57, 4977-4986.

CLEAVAGE AND
DEPROTECTION
1. Cleavage
For standard and UltraFast
deprotection protocols, cleave theoligo from the support using 2M
ammonia in methanol at room
temperature for 30 minutes.   (Onlyfor oligonucleotides greater than
50 nucleotides in length, rinse thesupport with a further volume ofwater.  Combine the two washes andevaporate to dryness.)
2. Deprotection
Standard
Add 1 volume of 30% ammoniumhydroxide, seal and deprotect using
the conditions appropriate forremoval of the protecting groups on
the nucleobases.
UltraFast
Add 1 volume of AMA (ammoniumhydroxide/40% aqueous methylamine
1:1) seal and deprotect at 65°C for 10
minutes.
UltraMild Using Ammonium Hydroxide
A d d 1 vo l u m e o f a m m o n i u mhydroxide, seal and leave at room
temperature for 8 hours.
UltraMild Cleavage and Deprotection
Using Potassium Carbonate in Methanol
Cleave the oligo from the support
using 50 mM potassium carbonate inmethanol at room temperature for 30
minutes.  Seal and leave overnight atroom temperature.

The key step in the use of any universal support in oligonucleotide synthesis is the dephosphorylation of the 3’-phosphategroup to form the desired 3’-hydroxyl group.  Azhayev1,2 has excelled in the investigation of neighboring group assistance inthe dephosphorylation reaction.  Amide groups may be considered to be weak N‑H acids and can display basic properties
in ammonium hydroxide or aqueous methylamine.  In the original work1,2, (±)-3-amino-1,2-propanediol was used to forma novel universal support (1).  A succinate linker attaches the 3-amino group to the support and the 2-OH is protected witha base-labile group to set up an amide assisted elimination in mildly basic conditions.  In this way, the dephos­­phor­ylation
reaction would eliminate the desired 3’-OH oligonucleotide into solution and the product of any ß-elimination competingside reaction would remain bound to the support.  A further improvement has been achieved by using a carbamate group
to connect the universal linker to the support, as in our product Universal Support III (2).  Using Universal Support III,  
an oligo yield of >80% can be achieved on polymeric supports, with purity equivalent to the same oligo prepared normally.
Conditions for Cleavage and Deprotection are outlined in the table opposite.  Universal Support III has been shown togenerate oligonucleotides with the same efficacy in polymerase extension reactions as regular oligos.  Despite the mild
elimination reaction, oligonucleotides up to 75mer in length can be prepared routinely without loss of oligo during thesynthesis cycles.  This support is also used for the production of siRNA oligos.

Item

Catalog No.

Pack

26-5010-01
26-5010-02
26-5010-10

0.1g
0.25g
1.0g

26-5110-41
26-5110-42
26-5110-45

Pack of 4
Pack of 4
Pack of 426-5110-13

Pack of 1

26-5210-41
26-5210-42
26-5210-45

Pack of 4
Pack of 4
Pack of 426-5210-14

Pack of 1

96 Well Format (MerMade, etc.)
Universal Support III PS
1 µmole columns
200 nmole columns
40 nmole columns

26-5110-91
26-5110-92
26-5110-95

Pack of 96
Pack of 96
Pack of 96

ABI 3900 Format
Universal Support III PS
200 nmole columns
40 nmole columns

26-5110-52
26-5110-55

Pack of 10
Pack of 10

Bulk Support
Universal Support III PS

ABI Format (not LV)
Universal Support III PS
1 µmole columns
0.2 µmole columns
40 nmole columns
10 µmole column (TWIST Format)
Expedite Format
1 µmole columns
0.2 µmole columns
40 nmole columns
15 µmole column (TWIST Format)

CHCl2
CHCl 2
O
DMTO

O

O
O

HN

NH
O

30

O

DTMO

Universal Support (1)

O

HN

H
N

O
Universal Support III (2)Q-SUPPORTS
Oligonucleotides are routinely prepared on supports to which the first nucleoside is attached via a succinate linkage.  
Over the years, the succinate linkage has demonstrated stability during the synthesis process but has sufficient lability to becleaved quickly in the deprotection step.  However, if the cleavage step is carried out with ammonium hydroxide manuallyor on the synthesizer, it consumes one hour of precious time while releasing only about 80% of the oligonucleotide.  
This step is, therefore, a bottleneck in the productivity of many synthesis groups.
Is it possible to find a replacement to the succinate group which offers good stability to the synthesis reagents while offeringa much faster cleavage step?  The oxalate group has been shown to be very labile during cleavage but its stability to thenormal synthesis reagents is not good, requiring changes for successful use.  In a practical but elegant study1 of various
bifunctional carboxylic acids, Richard Pon’s group identified hydroquinone-O,O’-diacetic acid as the most satisfactory
alternative to the succinate group.  Nucleosides with this linker arm (Q-linker) are attached to supports with the sameease as the succinyl linker arm.
The cleavage time in ammonium hydroxide at room temperature was found to be 2 minutes, but what about the stability
during synthesis?  How significant was premature cleavage of oligonucleotide on the synthesizer because of the basic
reagents in the capping mixes and oxidizer?  Pon showed that the Q-linker is stable to the capping reagents but very slightly
labile to the oxidizer (8% cleavage in overnight exposure which would correspond to about 2,000 normal synthesis cycles).
We tested the significance of premature cleavage by preparing sixteen 20mer oligonucleotides on a 0.2µmole scale, eightwith succinate and eight with Q-linkers.  The succinate supported oligos were cleaved for 1 hour at room temperature,
while those on the Q-support were cleaved for 2 minutes.  Both sets were then deprotected normally with ammoniumhydroxide.  The Q-supports actually gave 5% better yields of product than the succinate supports.  Oligo purities wereequivalent in both sets.
The Q-linker is absolutely compatible with all hydrolytic cleavage procedures, but especially mild procedures like potassium
carbonate in methanol.  Pon also showed that it is preferable for RNA supports, improving the cleavage time for 2’-silyl
protected nucleoside supports from 2 hours (60-65% cleavage) to 5 minutes (95% cleavage).

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

REFERENCE(1) R.T. Pon and S.Y. Yu, Tetrahedron Lett,
1997, 38, 3327-3330.

Q/SUCCINATE COMPARISON

We are offering Q-linkers of the four regular nucleosides on 500Å CPG in 0.2 and 1µmole scales.

Q-Support(2 minutes
cleavage)

Succinate(60 minutes
cleavage)

132 ODU*

125 ODU*

Average crude yield from eight
1µmole columns deprotected normally.

*

31

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGSUPPORTSSUPPORTS
Q-SUPPORTS (CONT.)
Catalog No.
dA

Catalog No.
dC

Catalog No.
Ac-dC

Catalog No.
dmf-dG

Catalog No.			
dT

Pack

500Å Bulk Support
21-2000-01
21-2000-02
21-2000-10

21-2010-01
21-2010-02
21-2010-10

21-2013-01
21-2013-02
21-2013-10

21-2029-01
21-2029-02
21-2029-10

21-2030-01
21-2030-02
21-2030-10

0.1g
0.25g
1.0g

ABI Format (not LV)
21-2100-41
21-2100-42

21-2110-41
21-2110-42

21-2113-41
21-2113-42

21-2129-41
21-2129-42

21-2130-41
21-2130-42

4X1µm
4X0.2µm

Expedite Format
21-2200-41
21-2200-42

21-2210-41
21-2210-42

21-2213-41
21-2213-42

21-2229-41
21-2229-42

21-2230-41
21-2230-42

4X1µm
4X0.2µm

NHBz

NHBz
N

N
DMTO

N

N

N

DMTO

O
O

O

O

O

O

dA-Q

N
O
O

O

O

NH

O

O

O

O

NH

dC-Q

O

NHAc
N
O

DMTO

N
O
O

O

O

O

NH

O

Ac-dC-Q

O

O
Me 2N

N

O

N

HN

N

N

DMTO

DMTO

O
O

O

O

O

O

dmf-dG-Q

32

CH 3

HN

NH

O

O

O

N

O

O

O
O

dT-Q

O

NH

O

HIGH LOAD CPG
Our high loading support is based on controlled pore silica and it retains the usual 500Å pores.  The spacer is also conventional.  
The only significant difference is the loading which is in the range 80 - 130µmoles/g or about 2.5 times the loading of normal500Å CPG.  Typical loadings for our high load CPG are in the 100 - 120µmoles/g range.  As a consequence of the high loading,this support should not be used for sequences longer than 40mers.  This high loading support is available in columns formost synthesizers.  The 2.5µmole column is identical to our standard 1µmole column (with the exception of the loading).  
It should be used on occasions when greater than 1µmole is desired but when a 10 or 15µmole synthesis is too high.  
It should be run using the 1µmole cycle.  The 25µmole column is identical to the 10µmole column used on Applied Biosystems
synthesizers.  It is run using the 10µmole cycle.  The 35µmole column is used as an alternative to the 15µmole Expedite
column.  Again no changes to the standard cycle are recommended.  The support is of course available in bulk for use on
large-scale synthesizers.  A word of caution is in order.  When using a column with a higher load than recommended by the
instrument manufacturer, there is a much smaller margin for error.  All reagents must be fresh and anhydrous diluent andactivator must be used.  Should you decide to prepare higher-loading columns, ensure that the molar excess of monomer
to support nucleoside is at least 5X and preferably 10X.

Item		

Catalog No.
dA			Columns

Catalog No.
dC

Catalog No.
dG

Catalog No.			
dT

(ABI)

25-2100-46
25-2100-17

25-2110-46
25-2110-17

25-2120-46
25-2120-17

25-2130-46
25-2130-17

4X2.5µm
1X25µm25-2200-46
25-2200-18

25-2210-46
25-2210-18

25-2220-46
25-2220-18

25-2230-46
25-2230-18

4X2.5µm
1X35µm25-2000-02
25-2000-10

25-2010-02
25-2010-10

25-2020-02
25-2020-10

25-2030-02
25-2030-10

0.25g
1.0g

(Expedite)Pack

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

RELATED
Glen UnySupport........................28

Bulk

NHBz

NHBz
N

N
DMTO

N

N

DMTO

O

O

C CH 2CH 2 CO

dA-CPG

O

N

O

lcaaCPGONOOC CH 2CH 2 CO

dC-CPG

O

lcaaCPG

HN

N

iBuHN
DMTO

N

N

O
HN
DMTO

O

O

C CH 2CH 2 CO

dG-CPG

O

lcaaCPG

O

CH 3

N
O

O

C CH 2CH 2 C

O

lcaaCPG

O

dT-CPG33

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLINGSUPPORTS

REAGENTS
ALTERNATIVE SOLVENTS/REAGENTS
ABBREVIATIONSAc2O = Acetic Anhydride
DCA = Dichloroacetic Acid
DCM = Dichloromethane
DMAP = Dimethylaminopyridine
I2 = Iodine
MeIm = 1-Methylimidazole
TCA = Trichloroacetic Acid
THF = Tetrahydrofuran

Item

Catalog No.

Pack

30-3040-10
30-3040-20
30-3040-25

1g
2g
25g

30-3140-45
30-3140-52
30-3140-57
30-3140-62
30-3142-52
30-3140-57

45mL
200mL
450mL
2L
200mL
450mL

4,5-Dicyanoimidazole (DCI), crystalline(Dissolve 1g in 34mL anhydrous
acetonitrile for a 0.25M solution)­
4,5-Dicyanoimidazole (DCI)(Dissolve 1g in 34mL anhydrous
acetonitrile for a 0.25M solution)

30-3050-1030-3050-25

1g
25g

30-3060-50
30-3060-30
30-3060-K5
30-3060-1K

5g
30g
500g
1000g

0.25M ,5-Dicyanoimidazole (DCI) in Acetonitrile(Applied Biosystems)

30-3150-45
30-3150-52
30-3150-57
30-3150-62
30-3152-52
30-3150-57

45mL
200mL
450mL
2L
200mL
450mL

5-Benzylthio-1H-tetrazole (BTT)(Dissolve 1g in 21.3mL anhydrous
acetonitrile for a 0.25M solution)

30-3070-1030-3070-20
30-3070-25

1g
2g
25g

0.25M 5-Benzylthio-1H-tetrazole in Acetonitrile(Applied Biosystems)

30-3170-45
30-3170-52
30-3170-57
30-3170-62
30-3172-52
30-3170-57

45mL
200mL
450mL
2L
200mL
450mL

Activator
5-Ethylthio-1H-tetrazole (ETT)(Dissolve 1g in 31mL anhydrous
acetonitrile for a 0.25M solution)

N N
N
N
H

CH 3CH 2S

Glen Research offers alternative solvents and reagents in suitable bottles and formulations for use on various DNA synthesizers.  
All solvents and reagents are prepared to our exacting specifications to ensure the highest coupling efficiencies and arepassed through a 0.2 micron filter during packaging to eliminate particulate contamination.   Glen Research offers theactivators below in powder form for later dissolution in anhydrous acetonitrile or as a prepared solution.

5-Ethylthio-1H-tetrazole

0.25M 5-Ethylthio-1H-tetrazole in Acetonitrile(Applied Biosystems)

CN

N
N
H

CN

(Expedite)

DCI

N N
PhCH 2S

N

N

H
5-Benzylthio-1H-tetrazole

O-

S
O

N

H+
N

N

O

(Expedite)

Saccharin 1-Methylimidazole

INTELLECTUAL PROPERTY
SMI is sold under license from Avecia
Biotechnology Inc.

(Expedite)

Saccharin 1-Methylimidazole (SMI)3430-3080
30-3180
30-3182

Discontinued
Discontinued
Discontinued

REAGENTS

Item

Catalog No.

Pack

40-4010-52
40-4010-57
40-4010-62

200mL
450mL
2L

40-4012-62

2L

40-4020-52

200mL

10% 1-Methylimidazole in Tetrahydrofuran

40-4120-52
40-4120-57
40-4120-62

200mL
450mL
2L

10% 1-Methylimidazole in Tetrahydrofuran/Pyridine (8:1)

40-4122-62

2L

Oxidizing Solution
0.02M Iodine  in Tetrahydrofuran/Pyridine/Water (70:20:10)

40-4132-62

2L

40-4032-52
40-4032-52E
40-4032-57
40-4032-62

200mL
200mL
450mL
2L

40-4040-57
40-4040-62

450mL
2L

40-4042-57
40-4042-62

450mL
2L

Cap Mix A
Tetrahydrofuran/2,6-Lutidine/Acetic Anhydride   

Tetrahydrofuran/Acetic Anhydride (9:1)   
Cap Mix B
6.5% Dimethylaminopyridine in Tetrahydrofuran(Cap B solutions containing DMAP are
preferred by some researchers
for preparing long oligos.)

0.02M Iodine  in Tetrahydrofuran/Pyridine/Water (88:20:2)(Low-Water Oxdizer)

Deblocking Mix
3% Dichloroacetic acid in Dichloromethane[Dichloroacetic acid (DCA) solutions are more
mildly acidic than the Trichloroacetic (TCA) equivalents,
possibly causing less depurination of dA sites.)
2.5% Dichloroacetic acid in Dichloromethane

MISCELLANEOUS RNA AND 2’-OMe-RNA MODIFICATION/LABELING MINOR BASES BACKBONE MODIFIERS STERLING

ALTERNATIVE SOLVENTS/REAGENTS (CONT.)

35

REAGENTS
CSO FOR NON-AQUEOUS OXIDATIONRELATED
0.1M CSO in PACE Chemistry.......41

INTELLECTUAL PROPERTYThis capping reagent is supplied underlicense.

CH3

H3C

O

S

N
O
O

O

The use of (1S)-(+)-(10-camphorsulfonyl)-oxaziridine (CSO) has been investigated as a non-aqueous oxidizer in DNA synthesis.
For example, we found that a 0.5M solution of CSO in acetonitrile worked well as an oxidizer for the synthesis of oligos
containing multiple incorporations of 7-deaza-dG, compared with iodine oxidation which caused substantial degradation.  
CSO has also worked well in the synthesis of a long poly-dI oligo, which could not be prepared using iodine oxidation due
to the sensitivity of the base.
CSO has been used for synthesizing oligos that incorporate the phosphonoacetate modification. A solution of 0.1M CSO is
recommended for the oxidation of PACE modifications as the phosphonite internucleotide linkage is more easily oxidized
than the phosphite internucleotide linkage. When synthesizing DNA-phosphonoacetate chimeric oligos, a 0.5M CSO solution
is recommended.

Item

CSO

O

Iodine-based oxidizers have been the standard for DNA and RNA synthesis since the advent of automated synthesizers.
They are fast and efficient oxidizers, typically requiring less than 30 seconds for complete oxidation of phosphite triesters tophosphate triesters. However, while iodine-based oxidizers work well for most applications, there are some circumstanceswhere non-aqueous oxidizers may be advantageous, especially where the bases or linkages being produced are sensitive
to the presence of water and/or iodine during synthesis.

O

P N(iPr)2O CNEtCatalog No.

Pack

40-4632-52
40-4632-52E
40-4632-57
40-4632-62(A minimum oxidation time of 3 minutes is required on small scales.)

200mL
200mL
450mL
2L

0.5M CSO in Anhydrous Acetonitrile (ABI)
0.5M CSO in Anhydrous Acetonitrile (Expedite)
0.5M CSO in Anhydrous Acetonitrile

UniCap Phosphoramidite

UNICAP PHOSPHORAMIDITE
The phosphoramidite of diethylene glycol monoethyl ether, UniCap, is the basis for an alternative capping reagent.  
To use UniCap as a capping amidite on the Expedite 8909 or AB synthesizers, dilute it to the standard amidite concentrationand place the vial in position 5 on the instrument.  Cycles can be modified by adding coupling steps for amidite reservoir 5
after the last column coupling step.  The standard capping steps can be left out of the cycle.  UniCap Phosphoramidite wasoriginally developed for oligo synthesis on the surface of chips and is the capping reagent of choice for this application.

36

Item

Catalog No.

Pack

UniCap Phosphoramidite

10-4410-02
10-4410-05
10-4410-10
10-4410-20

0.25g
0.5g
1.0g
2.0g

BACKBONE MODIFICATIONSULFURIZING REAGENTS

Sulfurizing Reagent II (3-((Dimethylamino-methylidene)amino)-3H-1,2,4-dithiazole-3-thione, DDTT) exhibits all the propertiesof Beaucage Reagent while adding stability in solution on the synthesizer AND offering strong ability to sulfurize RNA linkages.  
Sulfurizing Reagent II is available in powder form and as a stable solution.

Item

Catalog No.

Pack

Sulfurizing Reagent II (DDTT)(Dissolve at a concentration of 1g/100mL
to form an approximate 0.05M solution)

40-4037-10
40-4037-20

1g
2g

0.05M Sulfurizing Reagent II (DDTT) in Pyridine/Acetonitrile

40-4137-51
40-4137-52
40-4137-57

100mL
200mL
450mL

S
N

N

S
N

Sulfurizing Reagent II

37

S

BACKBONE MODIFIERS

Glen Research’s Sulfurizing Reagents are used to prepare phosphorothioate linkages using CE phosphoramidite chemistry.  
Each reagent exhibits the following attributes:
1) Reliably soluble, making them safe to use on automated synthesizers.
2) Reaction is fast (30 seconds), making the process convenient on small scales and readily amenable to scale-up.
3) Process is efficient, with better than 96% of the linkages being phosphorothioate and the remainder being phosphodiester.

BACKBONE MODIFICATION
5’-CE PHOSPHORAMIDITESOTHER INSTRUMENT TYPES

Glen Research 5’-CE (ß-cyanoethyl) Phosphoramidites are designed for the production of 5’-5’ or 3’-3’ linkages, useful inantisense studies, or to synthesize oligonucleotide segments in the opposite sense from normal synthesis (Reverse Synthesis),for structural studies.  These monomers are packaged in ABI-style vials (see note box).

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMade

E
A
M

Item

Catalog No.

Pack

dA-5’-CE Phosphoramidite

10-0001-02
10-0001-05
10-0001-10

0.25g
0.5g
1.0g

dC-5’-CE Phosphoramidite

10-0101-02
10-0101-05
10-0101-10

0.25g
0.5g
1.0g

Ac-dC-5’-CE Phosphoramidite

10-5101-02
10-5101-05
10-5101-10

0.25g
0.5g
1.0g

dmf-dG-5’-CE Phosphoramidite

10-9201-02
10-9201-05
10-9201-10

0.25g
0.5g
1.0g

dT-5’-CE Phosphoramidite

10-0301-02
10-0301-05
10-0301-10

0.25g
0.5g
1.0g

(Please inquire for availability of vials andcolumns for other instrument types.)

NHBz
N(iPr)2N

P O

CNEt O

N

N
O

ODMT

dA-5’-CE Phosphoramidite

38

O

NHBz
N

N
(iPr)2N

P O

CNEt OO(Me)2N

N

N
O

ODMT

dC-5’-CE Phosphoramidite

O
N

HN

N(iPr)2

P

CNEt

O

O

N

N
O
ODMT

AC-dC-5’-CE Phosphoramidite

Dmf-dG-5’-CE Phosphoramidite

HN(iPr)2N

P O

CNEt O

O

N
O

ODMT

dT-5’-CE Phosphoramidite

CH 3

BACKBONE MODIFICATION
5’-SUPPORTS

Item

Catalog No.

Pack

dA-5’-CPG

20-0002-01
20-0002-10
20-0012-41
20-0012-42
20-0012-13
20-0012-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-0102-01
20-0102-10
20-0112-41
20-0112-42
20-0112-13
20-0112-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-0202-01
20-0202-10
20-0212-41
20-0212-42
20-0212-13
20-0212-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-9202-01
20-9202-10
20-9212-41
20-9212-42
20-9212-13
20-9212-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-0302-01
20-0302-10
20-0312-41
20-0312-42
20-0312-13
20-0312-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)dC-5’-CPG
1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)dG-5’-CPG
1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)dmf-dG-5’-CPG
1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)dT-5’-CPG
1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

NHBz
N
CPG -lcaa-succinyl O

O

CPG -lcaa-succinyl O

O

N

HN

N

N

N

O

O

NHBz

N

N
O

iBuHN
CPG -lcaa-succinyl O(Me)2N

N

N
O

ODMT

ODMT

ODMT

dA-5’-CPG

dC-5’-CPG

dG-5’-CPG

CPG-lcaasuccinyl

O
N

HN
N
O

BACKBONE MODIFIERS

The following supports are used to produce oligonucleotides with nuclease resistant 3’-3’ linkages at the 3’ terminus (byattaching regular 3’-CE phosphoramidites) or to produce oligonucleotide sections in the opposite sense (by attaching 5’-CE
phosphoramidites).  ABI-style columns are supplied unless otherwise requested (see note box).

NNO

CPG -lcaa-succinyl O

HN
O

CH 3

N
O

ODMT

ODMT

dmf-dG-5’-CPG

dT-5’-CPG

39

BACKBONE MODIFICATIONMETHYL PHOSPHONAMIDITESREFERENCE(1) M.P. Reddy, F. Farooqui, and N.B.
Hanna, Tetrahedron Lett., 1996, 37,
8691-8694.

Methyl Phosphonamidites may be used in DNA synthesizers following conventional CE Phosphoramidite protocols to produce
oligonucleotides containing one or more methyl phosphonate linkages.  However, deprotection and purification techniques
differ and a description of the procedures is included in the Technical Bulletin.  We also offer the dC monomer with acetyl
base protection.1   This protecting group is removed with ammonium hydroxide during the cleavage step, eliminating
modification at the dC sites during the deprotection step using ethylenediamine in ethanol.

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMade

E
A
M

Item

Catalog No.

Pack

dA-Me Phosphonamidite

10-1100-02
10-1100-05

0.25g
0.5g

Ac-dC-Me Phosphonamidite

10-1115-02
10-1115-05

0.25g
0.5g

dG-Me Phosphonamidite

10-1120-02
10-1120-05

0.25g
0.5g

dT-Me  Phosphonamidite

10-1130-02
10-1130-05

0.25g
0.5g

(Please inquire for availability of vials andcolumns for other instrument types.)

NHBz
N
DMTO

N

N
O

O P N(iPr)2
CH 3

dA-Me Phosphonamidite

40

O

NHAc
N

DMTO

O

O
N

HN

N
N
O
O P N(iPr)2
CH 3

Ac-dC-Me Phosphonamidite

iBuHN
DMTO

HN

N

N
O

O P N(iPr)2
CH 3

dG-Me Phosphonamidite

DMTO

O

CH 3

N
O

O P N(iPr)2
CH 3

dT-Me Phosphonamidite

BACKBONE MODIFICATIONPACE PHOSPHORAMIDITESPACE monomers are fully soluble in acetonitrile at a recommended concentration of 0.1M and are compatible with standard
DNA synthesizers.  As an optimal cycle, we recommend using DCI as an activator (30-3150-XX) and a 15 minute couplingtime.  Following coupling, cap using Unicap (10-4410-XX) with a regular coupling time and then oxidize using 0.5M CSO
for 3 minutes.  Alternatively, a 33 minute coupling time using 0.45M tetrazole, oxidation using low-water iodine (40-4032XX) followed by capping with 6.5% DMAP as Cap B will give acceptable results.  For deprotection, pre-treat the synthesis
column with 1.5% DBU in anhydrous acetonitrile for 60 minutes at room temperature to remove 1,1-dimethyl-2-cyanoethyl
protecting groups. Rinse the column with acetonitrile, dry under argon and complete the deprotection with 40% aqueous
methylamine for 2 hours at room temperature.

Item

Catalog No.

Pack

dA-PACE Phosphoramidite

10-1140

Discontinued

Ac-dC-PACE Phosphoramidite

10-1150

Discontinued

dG-PACE Phosphoramidite

10-1160

Discontinued

dT-PACE Phosphoramidite

10-1170

Discontinued

INTELLECTUAL PROPERTY
These products are covered bypatent, US 7,067,641, and patents
pending owned by MetasenseTechnologies. Purchase of all or anyof these products includes a limited
license to use the products solely forthe manufacture of oligonucleotides
for research use only. This license
specifically excludes the use of
the product or oligonucleotides
containing the product for: (a)therapeutic or diagnostic applications(including kits, pools, libraries
and other products or services
that incorporate oligonucleotides
containing the product), (b) any invivo toxicity/safety study in supportof an investigational new drug
application (or foreign counterpart),or (c) resale (including sale of kits,
pools, libraries and other products orservices that incorporate the productor oligonucleotides containing the
product). If such activities havecommercial application, a separate
license is required from MetasenseTechnologies. Neither the product nor
any product created through its use
may be used in human clinical trials.
A simple agreement must be signed
before end-users and custom oligo
services may purchase these products
for use as defined above.  
https://www.glenresearch.com

RELATED
DCI...............................................34
UniCap........................................36
0.5M CSO....................................36
2’-OMe-PACE............................151

NHBz
N

N

O
O

P

N(iPr)2
O

iBuHN

N

O

DMTO

P

O

CN

P

O

O

O

N(iPr)2

CN

N

O
DTMO

O
O

N(iPr)2

CH3

HN

N

N

DMTO

O
O

O
N

HN

N

N

N
DMTO

O

NHAc

P

N(iPr)2
O

CN

CN

O

O

O

O

dA-PACE Phosphoramidite

Ac-dC-PACE Phosphoramidite

dG-PACE Phosphoramidite

dT-PACE Phosphoramidite

41

BACKBONE MODIFIERS

Phosphonoacetate (PACE) modified oligonucleotides show great potential as biological modifiers in a wide variety of
research applications.  PACE monomers are part of a family of Phosphonocarboxylate monomers.  The monomers can beeasily incorporated into complex oligonucleotides and are compatible with a wide variety of other sugar or heterobase
modifications.   PACE DNA can be conjugated through the carboxylic acid functional group. They have been shown to be
active in siRNA duplexes and accelerate the initial rate of cleavage by RNase H-1 when incorporated with phosphorothioates.  
However, the most interesting observation to date is that they exhibit an unprecedented enhancement in penetration ofcultured cells.

BACKBONE MODIFICATIONMETHYL PHOSPHORAMIDITESFor many years, Glen Research has supplied methyl phosphoramidites in addition to ß-cyanoethyl (CE) phosphoramidites
for the few situations where the more labile cyanoethyl group is not an advantage.  Some of our customers, probably
remembering that the methyl group was removed specifically with thiophenol, have tried to use these monomers to prepare
the interesting, uncharged, and nuclease-resistant methyl phosphotriester linkage.  Unfortunately, this linkage is labile toammonium hydroxide and the regular phosphodiester linkage is formed (along with a small amount of chain scission).  
We offer UltraMild methyl phosphoramidites for this application.  Oligos produced from these monomers can be deprotectedwith potassium carbonate in methanol to produce methyl phosphotriester linkages.  Since these linkages are diastereomericand uncharged, the oligos may be hard to handle.  Consequently, it is likely that chimeras will be produced using thesemonomers along with the regular UltraMild CE phosphoramidites.  If many dG residues are included in the oligonucleotide,
we recommend the use of phenoxyacetic anhydride (Pac2O) in Cap A.  This modification removes the possibility of exchangeof the isopropyl-phenoxyacetate (iPr-Pac) protecting group on the dG with acetate from the acetic anhydride capping mix.

Item

Catalog No.

Pack

Pac-dA-Me Phosphoramidite

10-1301-02
10-1301-05
10-1301-10

0.25g
0.5g
1.0g

Ac-dC-Me Phosphoramidite

10-1315-02
10-1315-05
10-1315-10

0.25g
0.5g
1.0g

iPr-Pac-dG-Me Phosphoramidite

10-1321-02
10-1321-05
10-1321-10

0.25g
0.5g
1.0g

dT-Me Phosphoramidite

10-1330-02
10-1330-05
10-1330-10

0.25g
0.5g
1.0g

Catalog No.

Pack

40-4210-52
40-4210-57

200mL
450mL

40-4212-52
40-4212-57

200mL
450mL

60-4600-30
60-4600-52
60-4600-57

30mL
200mL
450mL

ULTRAMILD SOLVENTS/REAGENTS
Item
Cap Mix A
THF/Pyridine/Pac2O  
(Applied Biosystems)		
THF/Pac2O   
(Expedite)
Deprotection Solution
0.05M Potassium Carbonate in Methanol
NHAcOPh
N
DMTO

N

N
O

O P N(iPr)2

42

NHAc

N

O CH 3

Pac-dA-Me Phosphoramidite

N
DMTO

O

O

O
N

HN
N

O
O P N(iPr)2
O CH 3Ac-dC-Me Phosphoramidite

iPr-PhOAcHN
DMTO

HN

N

N
O

O P N(iPr)2
O CH 3

iPr-Pac-dG-Me Phosphoramidite

O
DMTO

CH 3

N
O

O P N(iPr)2
O CH 3dT-Me Phosphoramidite

BACKBONE MODIFICATION
H-PHOSPHONATE MONOMERSItemCatalog No.

Pack

dA-H-Phosphonate, TEA Salt

10-1200

Discontinued

dC-H-Phosphonate, DBU Salt

10-1210

Discontinued

dG-H-Phosphonate, TEA Salt

10-1220

Discontinued

dT-H-Phosphonate, TEA Salt

10-1230

Discontinued

H-PHOSPHONATE REAGENTS
Our H-Phosphonate solvents and reagents have been discontinued.  H-Phosphonate reagents are easily prepared using
high purity products and the formulations shown below.

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

Item
1-Adamantanecarbonyl chloride is available from Aldrich, Catalog No. 117722. Dilute to 0.1M.
(Activator for monomers and capping reagent)

ABBREVIATIONSAcetonitrile/Pyridine (50:50), anhydrous(Monomer Diluent)I2 = Iodine
TEA = Triethylamine
THF = Tetrahydrofuran

Acetonitrile/Pyridine (95:5), anhydrous(Activator Diluent)
1% Isopropyl Phosphite in Acetonitrile/Pyridine (50:50)(Capping Reagent)
Acetonitrile/Pyridine (50:50)(Neutralizer and Wash Solvent)
4% I2 in Pyridine/H2O/THF (10:10:80)
THF/H2O/TEA (80:10:10)(Both reagents are required for oxidation of H-phosphonate linkages)

NHBz

NHBz
N

N
DMTO

N

N

DMTO

O
O

O P

O

N
O

O
-

H

+

O TEA

dA-H-Phosphonate

O P

O

O
N

HN

N

iBuHN
DMTO

HN

N

N

DMTO

O
O

-

H

O DBU

+

dC-H-Phosphonate

O P

O

CH 3

N
O

O
-

H

+

O TEA

dG-H-Phosphonate

O P

-

H

+

O TEA

dT-H-Phosphonate

43

BACKBONE MODIFIERS

OTHER INSTRUMENT TYPES

Our H-Phosphonate line has been discontinued.  Please contact Glen Support.

BACKBONE MODIFICATIONLOCKED ANALOG PHOSPHORAMIDITES AND SUPPORTS

REFERENCES(1a)A.A. Koshkin, S.K. Singh, P.
Nielsen, V.K. Rajwanshi, R. Kumar,
M. Meldgaard, C.E. Olsen, and J.
Wengel, Tetrahedron,1998, 54,
3607-3630.
(1b) S.K. Singh, P. Nielsen, A.A.
Koshkin, and J. Wengel, Chem.
Comm., 1998, (4), 455-456.
(2) L. Kværnø and J. Wengel, Chem.
Comm., 1999, (7), 657-658.
(3) P. Mouritzen, A.T. Nielsen,
H.M. Pfundheller, Y. Choleva, L.
Kongsbak, and S. Møller, Expert
Review of Molecular Diagnostics,
2003, 3(1), 27-38.

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M

Locked Nucleic Acid (LNA) was first described by Wengel and co-workers in 19981 as a novel class of conformationallyrestricted oligonucleotide analogues. LNA is a bicyclic nucleic acid where a ribonucleoside is linked between the 2’-oxygen
and the 4’-carbon atoms with a methylene unit. Oligonucleotides containing LNA exhibit unprecedented thermal stabilities
towards complementary DNA and RNA2, which allows excellent mismatch discrimination. In fact, the high binding affinity
of LNA oligos allows for the use of short probes in, for example, SNP genotyping3, allele specific PCR and mRNA sample
preparation. LNA is recommended for use in any hybridization assay that requires high specificity and/or reproducibility,e.g., dual labelled probes, in situ hybridization probes, molecular beacons and PCR primers. Furthermore, LNA offers thepossibility to adjust Tm values of primers and probes in multiplex assays. LNA can be mixed with DNA and RNA, as well asother nucleic acid analogues, modifiers and labels. LNA oligonucleotides are water soluble, and can be separated by gelelectrophoresis and precipitated by ethanol.
Glen Research is pleased to offer these highly useful reagents - Locked Analog (LA) Phosphoramidites and Supports - astools for this technology.

Item

Catalog No.

Pack

Bz-A-LA-CE Phosphoramidite

10-2000-05
10-2000-10

0.5g
1.0g

5-Me-Bz-C-LA-CE Phosphoramidite

10-2011-05
10-2011-10

0.5g
1.0g

dmf-G-LA-CE Phosphoramidite

10-2029-05
10-2029-10

0.5g
1.0g

T-LA-CE Phosphoramidite

10-2030-05
10-2030-10

0.5g
1.0g

(Please inquire for availability of vials andcolumns for other instrument types.)

NHBz

NHBz

N

N

N

N
DMTO

O

(Me)2N

N

HN
N

O

N

N

DMTO

N

O
DMTO

O

CH3

HN

O

O

O

O

O

O

O

P

N(iPr)2O

O

P

N(iPr)2

O

CNEt

P

N(iPr)2

P

O

CNEt

N(iPr)2

O

CNEt

O

CNEt

Bz-A-LNA

44

N

O
DMTO

O

O
CH3

N

5-Me-Bz-C-LNA

dmf-G-LNA

T-LNA

Item

Catalog No.

Pack

Bz-A-LA-CPG

20-2501-01
20-2501-02
20-2501-10
20-2501-41
20-2501-42
20-2501-13
20-2501-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2511-01
20-2511-02
20-2511-10
20-2511-41
20-2511-42
20-2511-13
20-2511-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2529-01
20-2529-02
20-2529-10
20-2529-41
20-2529-42
20-2529-13
20-2529-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2531-01
20-2531-02
20-2531-10
20-2531-41
20-2531-42
20-2531-14
20-2531-13

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)Bz-5-Me-C-LA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)dmf-G-LA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

T-LA-CPG

1 µmole columns
0.2 µmole columns
15 µmole column (Expedite)
10 µmole column (ABI)

Bz-A-LNA

5-Me-Bz-C-LNA

dmf-G-LNA

BACKBONE MODIFIERSBACKBONE MODIFICATION

T-LNA

45

BACKBONE MODIFICATION
BETA-L-DNA MONOMERSOTHER INSTRUMENT TYPES

beta L-DNA is the mirror image version of naturally occurring D-DNA. L-DNA and D-DNA share identical structures thatdiffer only in terms of stereochemistry and generally have identical physical and chemical properties. The difference intheir stereochemistry results in differences in their interactions with chiral molecules, D-DNA will only bind to its D-DNA
complement to form right-handed helices, and likewise, L-DNA will only bind to its L-DNA complement to form left-handed
helices. For this reason, enzymes that interact with D-DNA, including nucleases, typically won’t interact with L-DNA. The
unique properties of L-DNAs have made them attractive for many biological applications such as Aptamers, Molecular
Beacons, Molecular Tagging, and Drug Nanocarriers. Note that the procedure for synthesizing L-DNA oligonucleotides isvery similar to that of D-DNA oligonucleotides. Please see our Glen Report version 31.2 for more details.

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type
Expedite
Applied Biosystems 3900
MerMadeItem

Catalog No.

Pack

Add

beta-L-Pac-dA-CE Phosphoramidite

EA
M

beta-L-Ac-dC-CE Phosphoramidite

10-2101-02
10-2101-05
10-2101-10
10-2115-02
10-2115-05
10-2115-10
10-2121-02
10-2121-05
10-2121-10
10-2130-02
10-2130-05
10-2130-10

0.25g
0.5g
1.0g
0.25g
0.5g
1.0g
0.25g
0.5g
1.0g
0.25g
0.5g
1.0g

(Please inquire for availability of vials andcolumns for other instrument types.)beta-L-iPr-Pac-dG-CE Phosphoramidite

REFERENCES

beta-L-dT-CE Phosphoramidite(1) J. Nielsen, W.K.D. Brill, and M.H.
Caruthers, Tetrahedron Letters, 1988,
29, 2911-2914.
(2) L. Cummins, D. Graff, G. Beaton,
W.S. Marshall, and M.H. Caruthers,
Biochemistry, 1996, 35, 8734-41.
(3) X. Yang, and D.G. Gorenstein, Curr
Drug Targets, 2004, 5, 705-15.
(4) W.S. Marshall, and M.H. Caruthers,
Science, 1993, 259, 1564-70.
(5) J.L. Tonkinson, et al., Antisense
Research and Development, 1994, 4,
269-278.
(6) X. Yang, et al., Bioorg Med Chem Lett,
1999, 9, 3357-62.
(7) X. Yang, et al., Ann N Y Acad Sci,
2006, 1082, 116-9.
(8) X. Yang, et al., Nucleic Acids Res,
2002, 30, e132.

RELATED
2’-OMe-RNA
Thiophosphoramidites..............39
N

N
N

N

O
ODMT

O P

N(iPr)2

O CNEtbeta-L-Pac-dA

iPrPhOAcHN

N
O

ODMT

O P

O
N

HN

N

O

46

O

NHAc

NHAcOPh

N

HN

N

O
O

N(iPr)2

O P

N(iPr)2

O CNEtO CNEtbeta-L-Ac-dC

ODMT

beta-L-iPr-dG

N
ODMT

O

O P

N(iPr)2

O CNEtbeta-L-dT

MISCELLANEOUS

NOTES

47

OLIGONUCLEOTIDE-DIRECTED MUTAGENESISTRIMER PHOSPHORAMIDITESREFERENCES(1) A.L. Kayushin, M.D. Korosteleva,
A.I. Miroshnikov, W. Kosch,
D. Zubov, and N. Piel, Nucleic
Acids Research, 1996, 24,3748-3755.
(2) A. Kayushin, et al., Nucleos
Nucleot, 1999, 18, 1531-1533.
(3) A. Kayushin, M. Korosteleva,
and A. Miroshnikov, Nucleos
Nucleot Nucleic Acids, 2000,
19, 1967-1976.
(4) T. Mauriala, S. Auriola,
A. Azhayev, A. Kayushin,
M. Korosteleva, and A.
Miroshnikov, J Pharm Biomed
Anal, 2004, 34, 199-206.
(5) C. Neylon, Nucleic Acids Res,
2004, 32, 1448-59.
(6) L.R. Krumpe, K.M. Schumacher,
J.B. McMahon, L. Makowski,
and T. Mori, BMC Biotechnol,
2007, 7, 65-72.
(7) F.A. Fellouse, et al., J Mol Biol,
2007, 373, 924-40.
(8) W.P. Stemmer, A. Crameri, K.D.
Ha, T.M. Brennan, and H.L.
Heyneker, Gene, 1995, 164,49-53.
(9) P.M. Sharp, and W.H. Li, Nucleic
Acids Res, 1987, 15, 1281-95.

B1
DMTO

O

B2

O P O

O
O P O

OClPh

B3

OClPh

General Structure of Trimer
Phosphoramidites,
where B=Abz, Cbz, Gibu, T

OCEP

Trimer phosphoramidites1-4 have proven to be extremely valuable because they allow codon-based mutagenesis, which
circumvents the common problems of codon-bias, frame-shift mutations, and the introduction of nonsense or stop codons.5
This is accomplished by introducing a mixture of all 20 amino acid codons (or subset thereof) at any location within thesequenced to be mutated.  This leads to the production of clonal libraries of exceptional diversity with order-of-magnitude
increases in amino acid sequence variance while either maintaining a uniform amino acid distribution6 or one that is biased
toward a desired set of amino acids.7
However, difficulties arise when trying to introduce mutations in multiple distal regions of a gene simultaneously.
The synthesis of long oligonucleotides is required, which inevitably leads to lower sequence fidelity due to deletion mutants,
depurination events and, to a lesser extent, mutations arising from deamination of cytidine, for example.
An elegant solution to this problem is the use of Antisense Trimer Phosphoramidites. These trimers are the reverse
complement of the cannonical ‘sense’ codons. When these antisense codons are put into the noncoding strand of atemplate DNA and amplified by PCR, they will code for the sense codon in the opposite strand of DNA. This allows thepowerful technique of PCR Assembly8 to generate not only kilobase-sized genes from short 50mer oligonucleotides, but tosimultaneously mutate multiple distal regions of that gene, as shown in Figure 1.
The sense and their corresponding antisense codons are listed in Table 1. Conveniently, many of our existing sense trimers
can act as antisense codons. For example, AAC, which codes for asparagine, has the anticodon GTT, which is the sense codon
for valine. However, some of the existing trimers, while they can act as an antisense codon, are not good choices for use.
For example, TGG, which codes for tryptophan, could be used as an antisense codon for proline because CCA is one ofproline’s synonymous codons. However, CCA has a relatively low Codon Adaptation Index (CAI) value9 in E. coli, which could
limit protein expression in that commonly used organism. For this reason, the anticodon CGG was chosen for optimal
expression in E. coli, as were the other new antisense codons shown in bold in Table 1.
Included in Table 1 are the reaction factors (RFs) for each of the sense and antisense trimers. The reaction factor is criticalsince the trimers will likely be mixed and they exhibit different rates of reaction when coupling during oligonucleotide
synthesis. An example where the RF is used to compensate for differing rates of coupling follows.  The RF for AAC is 1.0
and for TAC is 1.6. Therefore, 1.6 equivalents of TAC are needed for every 1.0 equivalent of AAC for equal coupling rates.
So to obtain 25 umoles of trimer mix that yields, on average, a 1:1 ratio of AAC/TAC at the mutation site, 9.6 umoles of AAC
would be added to 15.4 umoles of TAC.
All of the trimers are available individually so the researchers can prepare custom trimer mixes.  Two pre-made catalog
trimer mixes are available:  13-1991-xx, for incorporating all 20 amino acid codons equally into a sequence and 13-1992-xx,
for incorporating 19 amino acid codons (-Cys). For a custom trimer mix of a particular subset of codons or a trimer mix that
represents a set of trimers that is biased toward a particular codon or codons, please contact support@glenresearch.com
for a quotation and projected delivery date.
There is a concern that the sequence of the trimers has to be verified.  For example, CAT coding for histidine, has to bedifferentiated from TAC, coding for tyrosine.  These two trimers have virtually identical lipophilicity and their identity cannot
be clearly confirmed by HPLC.  This problem has been solved4 using HPLC electrospray mass spectrometric analysis of thetrimers, which provides data confirming molecular weight and sequence.

48

OLIGONUCLEOTIDE-DIRECTED MUTAGENESIS
Figure 1: Simultaneous Mutation of Multiple Distal Regions of Gene
NHBz
N

N

Pool of Oligos
DMTO

N

N

O

O

CH 3

HN
O
O P O
O

PCR

O

N

NHBz

O

Cl

N
O

O

TABLE 1: RF of Trimer Phosphoramidites

AAA (Lys)
AAC (Asn)
ACT (Thr)
ATC (Ile)ATG (Met)
CAG (Gln)
CAT (His)
CCG (Pro)CGT (Arg)
CTG (Leu)
GAA (Glu)
GAC (Asp)
GCT (Ala)
GGT (Gly)GTT (Val)TAC (Tyr)
TCT (Ser)TGC (Cys)
TGG (Trp)
TTC (Phe)

O

N
O

Cl

Reaction
Factor (RF)
1.10
1.00
1.60
1.50
1.30
2.00
1.30
1.80
1.40
1.20
1.40
1.60
1.50
1.10
1.90
1.60
1.30
1.50
1.10
1.30

O P N(iPr)2

Antisense codons
Reaction(5’->3’)		Factor (RF)
TTT
GTT
GGT
GAT
CAT
CTG
ATG
CGG
GCG
CAG
TTC
ATC
TGC
ACC
AAC
GTA
AGA
GCA
CCA
GAA

1.70
1.90
1.10
1.40
1.30
1.20
1.30
0.80
0.60
2.00
1.30
1.50
1.50
0.90
1.00
1.50
1.40
1.00
1.10
1.40

O CNEtATC Trimer

49

MINOR BASES

Sense codons(5'->3')PO

O

OLIGONUCLEOTIDE-DIRECTED MUTAGENESIS
Item

Catalog No.

Pack

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Sense Trimers
AAA Trimer Phosphoramidite(Lys)

13-1000-95
13-1000-90

50 µm
100 µm

AAC Trimer Phosphoramidite(Asn)13-1001-95
13-1001-90

50 µm
100 µmMonomers
For Instrument typeAdd

ACT Trimer Phosphoramidite(Thr)

13-1013-95
13-1013-90

50 µm
100 µmExpedite
MerMadeE
M

ATC Trimer Phosphoramidite(Ile)13-1031-95
13-1031-90

50 µm
100 µmColumns
For Instrument type

Add

ATG Trimer Phosphoramidite(Met)13-1032-95
13-1032-90

50 µm
100 µmExpedite
Applied Biosystems 3900
MerMadeEAM

CAG Trimer Phosphoramidite(Gln)13-1102-95
13-1102-90

50 µm
100 µm

CAT Trimer Phosphoramidite(His)13-1103-95
13-1103-90

50 µm
100 µm

CCG Trimer Phosphoramidite(Pro)13-1112-95
13-1112-90

50 µm
100 µm

CGT Trimer Phosphoramidite(Arg)13-1123-95
13-1123-90

50 µm
100 µm

CTG Trimer Phosphoramidite(Leu)

13-1132-95
13-1132-90

50 µm
100 µmGAA Trimer Phosphoramidite(Glu)

13-1200-95
13-1200-90

50 µm
100 µmGAC Trimer Phosphoramidite(Asp)13-1201-95
13-1201-90

50 µm
100 µmGCT Trimer Phosphoramidite(Ala)13-1213-95
13-1213-90

50 µm
100 µmGGT Trimer Phosphoramidite(Gly)13-1223-95
13-1223-90

50 µm
100 µm

GTT Trimer Phosphoramidite(Val)13-1233-95
13-1233-90

50 µm
100 µmTAC Trimer Phosphoramidite(Tyr)13-1301-95
13-1301-90

50 µm
100 µm

TCT Trimer Phosphoramidite(Ser)13-1313-95
13-1313-90

50 µm
100 µmTGC Trimer Phosphoramidite(Cys)

13-1321-95
13-1321-90

50 µm
100 µm

TGG Trimer Phosphoramidite(Trp)13-1322-95
13-1322-90

50 µm
100 µmTTC Trimer Phosphoramidite(Phe)13-1331-95
13-1331-90

50 µm
100 µmTrimer Phosphoramidite Mix 1(Mix of above 20 trimers)

13-1991-95
13-1991-90

50 µm
100 µmTrimer Phosphoramidite Mix 2(Mix of above 20 trimers less TGC-Cys)

13-1992-95
13-1992-90

50 µm
100 µm(Please inquire for availability of vials andcolumns for other instrument types.)

50

Item

Catalog No.

Pack

Antisense Trimers
AAC Trimer Phosphoramidite(Anti Val)

13-1001-95
13-1001-90

50 µm
100 µmACC Trimer Phosphoramidite(Anti Gly)

13-1011-95
13-1011-90

50 µm
100 µmAGA Trimer Phosphoramidite(Anti Ser)

13-1020-95
13-1020-90

50 µm
100 µm

ATC Trimer Phosphoramidite(Anti Asp)

13-1031-95
13-1031-90

50 µm
100 µm

ATG Trimer Phosphoramidite(Anti His)

13-1032-95
13-1032-90

50 µm
100 µm

CAG Trimer Phosphoramidite(Anti Leu)

13-1102-95
13-1102-90

50 µm
100 µm

CAT Trimer Phosphoramidite(Anti Met)

13-1103-95
13-1103-90

50 µm
100 µmCCA Trimer Phosphoramidite(Anti Trp)

13-1110-95
13-1110-90

50 µm
100 µm

CGG Trimer Phosphoramidite(Anti Pro)

13-1122-95
13-1122-90

50 µm
100 µmGAA Trimer Phosphoramidite(Anti Phe)

13-1200-95
13-1200-90

50 µm
100 µmGAT Trimer Phosphoramidite(Anti Ile)

13-1203-95
13-1203-90

50 µm
100 µmGCA Trimer Phosphoramidite(Anti Cys)

13-1210-95
13-1210-90

50 µm
100 µm

GCG Trimer Phosphoramidite(Anti Arg)

13-1212-95
13-1212-90

50 µm
100 µmGGT Trimer Phosphoramidite(Anti Thr)

13-1223-95
13-1223-90

50 µm
100 µmGTA Trimer Phosphoramidite(Anti Tyr)

13-1230-95
13-1230-90

50 µm
100 µmTGC Trimer Phosphoramidite(Anti Ala)

13-1321-95
13-1321-90

50 µm
100 µmTTC Trimer Phosphoramidite(Anti Glu)

13-1331-95
13-1331-90

50 µm
100 µm

TTT Trimer Phosphoramidite(Anti Lys)

13-1333-95
13-1333-90

50 µm
100 µmMINOR BASES

OLIGONUCLEOTIDE-DIRECTED MUTAGENESIS

51

DUPLEX STABILITY MODIFICATIONBASES AFFECTING DUPLEX STABILITY
Substitution of C-5 propynyl-dC (pdC) for dC and C-5 propynyl-dU (pdU) for dT are effective strategies to enhance basepairing. Using these base substitutions, duplex stability and melting temperatures are raised by the following amounts: C-5
propynyl-C 2.8° per substitution; C-5 propynyl-U 1.7° per substitution.  AP-dC (G-clamp) substitutes for dC and is anothervery important modified nucleoside that enhances hybridization by 7-21° per substitution depending upon the sequenceand location of the AP-dC.  The ability of these modified bases to enhance binding while maintaining specificity has provenuseful in antisense research and in the synthesis of high affinity probes.  AP-dC is also a fluorescent nucleoside and shouldfind uses in DNA structural research.
dW is a C-nucleoside that acts as a strong adenine base paring analog. In addition to the typical two hydrogen bonds foundbetween T and A, dW can also interact with A via van der Waals forces. The result is a dW–A interaction that approaches
the strength of a C–G base pair while also exhibiting enhanced base-pairing fidelity. dW can be used in place of T as a single
substitution or a complete replacement for oligonucleotide hybridization applications.

Item

Catalog No.

Pack

pdC-CE Phosphoramidite

10-1014-90
10-1014-02
10-1014-05

100 µmole
0.25g
0.5g

pdU-CE Phosphoramidite

10-1054-90
10-1054-02
10-1054-05

100 µmole
0.25g
0.5g

AP-dC-CE Phosphoramidite(G-Clamp)

10-1097-95
10-1097-90
10-1097-02

50 µmole
100 µmole
0.25g

dW-CE Phosphoramidite

10-1527-95
10-1527-90
10-1527-02

50 µmole
100 µmole
0.25g

C-5 methyl pyrimidine nucleosides are known to stabilize duplexes relative to the non-methylated bases.   Therefore,
enhanced binding can be achieved using 5-methyl-dC in place of dC, duplex melting temperature being increased by 1.3°.  
Ac-5-Me-dC-CE Phosphoramidite is fully compatible with AMA deprotection and none of the N4-Me transamination mutant
is observed on deprotection.  
Item

Catalog No.

Pack

5-Me-dC-CE Phosphoramidite

10-1060-90
10-1060-02

100 µmole
0.25g

Ac-5-Me-dC-CE Phosphoramidite

10-1560-90
10-1560-02

100 µmole
0.25g

O

N

N(iBu)2

N
DMTO

O

O

N

O P N(iPr)2
O CNEt

pdC

52

O

CH 3

HN
DMTO

O

O

F3C

OPiv

CH 3

N

O CNEt

pdU

DMTO

TIPS

O

O

P

N(iPr)2

O

CNEt

dW

DMTO

O

N
O

O P N(iPr)2
O CNEt

AP-dC

CH 3

N

O

N

NHAc

NHBz

HN

N

O P N(iPr)2

O

NH

DMTO

O

N
O

O P N(iPr)2
O CNEt

5-Me-dC

CH3

N
N

O

DMTO

O
O

P

N(iPr)2O

CNEt

Ac-5-Me-dC

DUPLEX STABILITY MODIFICATIONBASES AFFECTING DUPLEX STABILITY (CONT.)

Item

Catalog No.

Pack

2-Amino-dA-CE Phosphoramidite(2,6-diaminopurine)

10-1085-95
10-1085-90
10-1085-02

50 µmole
100 µmole
0.25g

Pac-2-Amino-dA-CE Phosphoramidite(2,6-diaminopurine)

10-1585-95
10-1585-90
10-1585-02

50 µmole
100 µmole
0.25g

Sequences with high GC content may contain mismatches and still hybridize because of the high stability of the G-C basepair.  The N4-ethyl analogue of dC (N4-Et-dC) hybridizes specifically to natural dG but the stability of the base pair is reduced
to about the level of an AT base pair.
Coupling N6-Me-dA (10-1003) and N4-Et-dC (10-1068) with 1H-tetrazole leads to a trace of branching at the secondaryamine positions, while DCI leads to around 15% branching. In collaboration with Berry and Associates, the acetyl protected
monomers were prepared.   Acetyl protection was chosen since it would block branching reactions.   Oligonucleotides
synthesized using these monomers proved to be compatible with all popular deprotection strategies from UltraMild to
UltraFast.  When the acetyl protected monomers were compared with the unprotected monomers using DCI as activator,
branching was reduced from 15% to zero.
Item

Catalog No.

Pack

N4-Et-dC-CE Phosphoramidite

10-1068-95
10-1068-90
10-1068-02

50 µmole
100 µmole
0.25g

N4-Ac-N4-Et-dC-CE Phosphoramidite

10-1513-95
10-1513-90
10-1513-02

50 µmole
100 µmole
0.25g

N6-Me-dA-CE Phosphoramidite

10-1003-90
10-1003-02

100 µmole
0.25g

N6-Ac-N6-Me-dA-CE Phosphoramidite

10-1503-90
10-1503-02

100 µmole
0.25g

N(iBu)2

N(iBu)2N

N
N
DMTO

O
O P N(iPr)2
O CNEt2-Amino-dA

PhOAcHN
DMTO

N

N
O
O

P

N(iPr)2O

CNEt

Pac-2-Amino-dA

Et

NH Et

NAc

N

N

N

N

N

N(nBu)2

N

N

DMTO

O

N

N
O

O P N(iPr)2
O CNEtN4-Et-dC

N

O

DMTO

O
O

P

N(iPr)2O

CNEt

N4-Ac-N4-Et-dC

DMTO

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

NAc

N

O
O P N(iPr)2
O CNEt

N6-Me-dA

N

N

N

N

0.5M CSO....................................36
N6-Me-dA...................................39

Me

NHMe
N

RELATED

N

N
DMTO

O
O

P

N(iPr)2O

CNEt

N6-Ac-N6-Me-dA

53

MINOR BASES

The simplest approach to the design of high affinity primers and probes is to substitute A sites with 2-amino-A, since the2-amino-A-T base pair is equivalent in strength to the G-T base pair.  2-Amino-A also destabilizes A-G wobble mismatches,
thus increasing specificity.  In 1998, we introduced a 2-amino-dA monomer which exhibits fast and effective deprotectionin ammonium hydroxide and it is stabilized to depurination during synthesis.  We now recommend the use of 0.5 M CSO
in anhydrous acetonitrile (40-4632-xx) for best results with multiple additions of 2-amino-dA.   This is because the bis
formamidine protected 2-amino-dA leads to significant strand scission when standard iodine oxidation is used during
synthesis.  For this reason, we have also added Pac-2-Amino-dA, a monomer with optimized protection to meet the following
criteria: stable during oligonucleotide synthesis, oxidation, and detritylation; labile towards common deprotection conditions(NH3, AMA, MeNH2); and the nucleobase protecting groups are cleaved under fairly mild conditions.

DUPLEX STABILITY MODIFICATION
ZIP NUCLEIC ACIDS (ZNA®)INTELLECTUAL PROPERTY”Spermine phosphoramidite”
synthon is the subject matter ofU.S. Divisional Patent Application
No. 14/745,871, European Patent
No. 1973927 and foreign equivalents
for which Polyplus-transfection isthe co-owner. Product is sold forresearch purposes only.  Productshall not be used to manufactureoligospermine-oligonucleotide
conjugates for use in diagnostics,
clinical or commercial applications
including use in humans. There is
no implied license to manufactureoligospermine-oligonucleotide
conjugates for diagnostic, clinical,
or commercial applications,
including but not limited to contract
research. Please contact Polyplustransfection at licensing@polyplustransfection.com to obtain a license
for such use.
ZNA® is a registered trademark of
Polyplus-transfection SA.

RELATED
2-Amino-dA................................53
Pac-2-Amino-dA.........................53
2-Thio-dT....................................64
dmf-5-Me-isodC.........................59
dmf-isodG...................................59

Spermine phosphoramidite is used to produce oligospermine-oligonucleotide conjugates - Zip Nucleic Acids (ZNA®) Oligos.  
The name reflects the presumed mode of action.  The conjugates are believed to use the oligospermine to seek out andmove along (scan) oligonucleotide strands until the probe complementary sequence is located. The oligospermine thenperforms the function of stabilizing the formed duplex by reducing electrostatic repulsion, thereby leading to significantly
increased binding affinities.   ZNA® Oligos have found use in the following applications: Multiplex PCR; PCR of AT-richRegions; RT qPCR; Detection of MicroRNA; Improved SNP Discrimination; and Antisense and Antigene Effects.  Spermine
phosphoramidite is simple to use in oligonucleotide synthesis and can be added multiple times at the 3’ or 5’ terminus.  
Deprotection and isolation are also straightforward.  HPLC analysis of the conjugates requires high pH to suppress theionization of the spermine residues.
Item

Catalog No.

Pack

Spermine Phosphoramidite

10-1939-95
10-1939-90
10-1939-02

50 µmole
100 µmole
0.25g

CDPI3 MGB™ LABELING
Synthetic oligonucleotides with covalently-attached CDPI3 have enhanced DNA affinity and improved the hybridization
properties of sequence-specific DNA probes. Short CDPI3-oligonucleotides hybridize with single-stranded DNA to give morestable DNA duplexes than unmodified ODNs of similar length.  The simplest approach to MGB probe design is to use an MGB
support, add a quencher molecule as the first addition and complete the synthesis with a 5’-fluorophore.  Alternatively, a
fluorophore support could be used with the 5’ terminus containing a quencher molecule followed by a final MGB additionat the 5’ terminus.  Glen Research offers 5’-CDPI3 MGB™ Phosphoramidite and 3’-CDPI3 MGB™ CPG.  

SELECTIVELY BINDING COMPLEMENTARY (SBC) OLIGOS
SBC oligos exhibit high affinity for natural oligonucleotides but they show little affinity for other SBC oligos even of acomplementary sequence.  Oligos in which A has been replaced with 2-amino-A and T with 2-thio-T represent an excellent
example of SBC oligos.  While 2-amino-A forms a very stable base pair with T containing three hydrogen bonds, the stabilityof the base pair with 2-thio-T is greatly diminished. However, 2-thio-T base pairs perfectly well with A. As an example, SBC
20mers annealed against a DNA 20mer target exhibited Tm values 10 °C higher than the corresponding DNA-DNA hybrid,
whereas the SBC-SBC hybrid yielded Tm values 30 °C lower.

UNNATURAL BASE PAIRS
Unnatural base pairs display unique abilities in duplex DNA and in nucleic acid and protein biosyntheses.  A standard Watson
and Crick base pair is formed between iso-C and iso-G, but the hydrogen bonding pattern is quite different from the naturalbase pairs A-T and C-G. Iso-bases can, therefore, increase specificity of nucleic acid hydridization when introduced as a thirdbase pair. It has also been demonstrated that iso-bases 5-Me-iso-dC and iso-dG can function as degenerate pyrimidine
and purine bases, respectively. Iso-dG further functioned as a degenerate base opposite B (C, T, and G) ambiguous sites.

DMTO

N
TFA

N
TFA

TFA
N

Spermine Phosphoramidite

54

TFA
N

O

P

N(iPr)2O

CNEt

DUPLEX STABILITY MODIFICATIONCAPS FOR INCREASED DUPLEX STABILITY AND BASE-PAIRING FIDELITYNew  cap structures allow for the preparation of hybridization probes with increased affinity for complementary sequences.  
The  monomers used to prepare capped oligonucleotides are phosphoramidites that can be readily introduced via automated
DNA synthesis at the end of solid phase syntheses.  The caps favor the formation of stable Watson-Crick duplexes by stacking
on the terminal base pair (Figures Uaq
1 and2).  pore glass
oligonucleotide
controlled
capped duplex
chain

NH
DMT-O

Unmodified DNA:fraying and wobblingat the terminus

O

O

N

O

cap

B

O
O

O HN
O

O

O

O

terminal baseH or OH

PO2
Duplex with
cap-bearing probe

NH

O

O

O

O

N

O

Uaq capOCap(1) Dogan, Z.; Paulini, R.; Rojas Stütz,
J. A.; Narayanan, S.; Richert, C. J.
Amer. Chem. Soc. 2004, 126, 47624763.
(2) Narayanan, S.; Gall, J.; Richert, C.
Nucleic Acids Res. 2004, 32, 29012911.
(3) A. Patra, C. Richert, J. Amer. Chem.
Soc., 2009, 131, 12671-12681.
(4) C. Ahlborn, K. Siegmund, C. Richert,
J. Amer. Chem. Soc., 2007, 129,
15218-15232.

HO HN

HN

FIGURE 1: STACKING OF CAP ON 5’ TERMINAL BASE PAIRO OF Uaq CAP ON 3’ TERMINAL BASE PAIR
FIGURE 2:OSTACKING

Melting point increases of over 10 °C per modification can be realized for short duplexes.1,2  The caps fit canonical WatsonCrick base pairs and do not stack well on mismatched base pairs.  This leads to increased base pairing selectivity at theterminal and the penultimate position of oligonucleotides featuring the caps.  Base pairing fidelity is usually low at thetermini, where fraying occurs frequently in the absence of caps.  The beneficial effects of the caps are also realized whenlonger target strands are bound, so there is no need for blunt ends for the duplexes formed.1,2  The caps, when attached to
the 5’ terminus of an oligonucleotide, also facilitate purification as their lipophilicity leads to prolonged retention on reversed
phase columns or cartridges.  Finally, capping of termini may discourage the degradation of oligonucleotides by exonucleases.
3’-Uaq Cap CPG, a Uridine support modified with a 2’- anthraquinone residue, is the most effective oligonucleotide cap
known to date.3,4  For short hybrid duplexes between DNA probes and RNA target strands, the increase in Tm is up to 18 °C
and the modification is effective in increasing the Tm of DNA:DNA, RNA:RNA, and DNA:RNA hybrid duplexes.  3’-Uaq Cap
also increases probe specificity by depressing the melting point of terminal mismatches.

Item

Catalog No.

Pack

5’-Trimethoxystilbene Cap Phosphoramidite

10-1986-90
10-1986-02

100 µmole
0.25g

5’-Pyrene Cap Phosphoramidite

10-1987-90
10-1987-02

100 µmole
0.25g

3’-Uaq Cap CPG

20-2980-01
20-2980-10
20-2980-41
20-2980-42
20-2980-13
20-2980-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

O
HN

O

N

O

NH

DMTO

O P N(iPr)2OOO CNEt

MeO

N

MeO

O P N(iPr)2
O CNEtOMe

5’-Trimethoxystilbene Cap

5’-Pyrene Cap

O

HN
O

O

succinyl-CPG

3’-Uaq Cap CPG

55

MINOR BASESOREFERENCESEPIGENETICSDNA METHYLATIONRELATEDOne of the fastest growing fields in biology and cancer research is epigenetics.  While the underlying genetic code defines
which proteins and gene products are synthesized, it is epigenetic control that defines when and where they are expressed.
This dynamic control of gene expression is essential for X chromosome inactivation, embryogenesis, cellular differentiation
and appears integral to memory formation and synaptic plasticity.

5-Me-dC......................................52
5-hmdU.......................................67

In 2009, two reports1,2 described the discovery of 5-hydroxymethyl-2’-deoxyCytidine (hmdC), a novel dC modification in
Purkinje neurons and embryonic stem cells. Later, a third report found this modification to be strongly enriched in brain
tissues associated with higher cognitive functions.3 This dC modification is generated by the action of a-ketoglutarate
dependent ten eleven translocation (TET) enzymes, which oxidizes 5-Me-dC to hmdC. This finding stimulated discussion
about active demethylation pathways that could occur, e.g., via base excision repair (BER), with the help of specialized DNA
glycosylases. Alternatively, one could envision a process in which the hydroxymethyl group of hmdC is further oxidized to
5-formyl-dC (fdC) or 5-carboxy-dC (cadC) followed by elimination of either formic acid or carbon dioxide4,5.

REFERENCES(1) S. Kriaucionis, and N. Heintz, Science,
2009, 324, 929-30.
(2) M. Tahiliani, et al., Science, 2009,
324, 930-935.
(3) M. Münzel, et al., Angewandte
Chemie-International Edition, 2010,
49, 5375-5377.
(4) D. Globisch, et al., PLoS One, 2010,
5, e15367.
(5) S.C. Wu, and Y. Zhang, Nat Rev Mol
Cell Biol, 2010, 11, 607-20.
(6) M. Münzel, D. Globisch, C. Trindler,
and T. Carell, Org Lett, 2010, 12,5671-3.
(7) A.S. Schroder, et al., Angewandte
Chemie-International Edition, 2014,
53, 315-318.

Glen Research has supported this research since its inception by providing the building blocks for the synthesis ofoligonucleotides containing all the new dC derivatives - hmdC, fdC and cadC. The first generation hmdC phosphoramidite
was fairly very well accepted but requires fairly harsh deprotection conditions. Therefore, a second generation building
block (5-Hydroxymethyl-dC II) developed by Carell and co-workers that is compatible with UltraMild deprotection was
introduced.6  5-Formyl-dC III has been designed to meet all of the requirements to prepare an oligo containing all of themethylated variants.7
Item

Catalog No.

Pack

5-Hydroxymethyl-dC-CE Phosphoramidite

10-1062-95
10-1062-90
10-1062-02

50 µmole
100 µmole
0.25g

5-Carboxy-dC-CE Phosphoramidite

10-1066-95
10-1066-90
10-1066-02

50 µmole
100 µmole
0.25g

5-Formyl-dC-CE Phosphoramidite

10-1514-95
10-1514-90
10-1514-02

50 µmole
100 µmole
0.25g

5-Hydroxymethyl-dC II-CE Phosphoramidite

10-1510-95
10-1510-90
10-1510-02

50 µmole
100 µmole
0.25g

5-Formyl-dC III-CE Phosphoramidite

10-1564-95
10-1564-90
10-1564-02

50 µmole
100 µmole
0.25g

O

O
HN

NHBz
CH2-O-CNEt

N

O
O

56

N

O

DMTO

P

N(iPr)2O

CNEt

5-Hydroxymethyl-dC

NHBz

O

N

O

DMTO

O
O

CO2Et

N

N

P

N(iPr)2O

CNEt

5-Hydroxymethyl-dC II

N

O

DMTO

O
O

P

N(iPr)2O

CNEt

5-Carboxy-dC

NH

NHAc OAc OAc
N
N

O

DMTO

O

P

N(iPr)2O

CNEt

5-Formyl-dC

N

O

DMTO

O

O

N

MeO

O
O

O

P

N(iPr)2O

CNEt

5-Formyl-dC III

PCR/SEQUENCING APPLICATIONSDUPLEX EFFECTS

The modified bases designated P and K show considerable promise as degenerate bases.  The pyrimidine derivative P, whenintroduced into oligonucleotides, base pairs with either A or G, while the purine derivative K base pairs with either C or T.  
A dP+dK mix also can serve as a mixed base with much less degeneracy than dA+dC+dG+dT (N).

Item

Catalog No.

Pack

dA+dG-CE Phosphoramidites
dC+dT-CE Phosphoramidites
dA+dC+dG+dT-CE Phosphoramidites

10-1002-02
10-1013-02
10-1023-02

0.25g
0.25g
0.25g

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

Other pack sizes, mixed base combinations and custom doping of individual monomers are available on request.  
Also, mixed base columns are available in 0.2 and 1.0 µmole sizes on request.
dI-CE Phosphoramidite

10-1040-90
10-1040-02

100 µmole
0.25g

dI-CPG 500
1 µmole columns
0.2 µmole columns

20-2040-01
20-2190-41
20-2190-42

0.1g
Pack of 4
Pack of 4

dI-CPG 1000
1 µmole columns
0.2 µmole columns

20-2041-01
20-2191-41
20-2191-42

0.1g
Pack of 4
Pack of 4

dU-CE Phosphoramidite

10-1050-90
10-1050-02

100 µmole
0.25g

dU-CPG 500
1 µmole columns
0.2 µmole columns

20-2050-01
20-2150-41
20-2150-42

0.1g
Pack of 4
Pack of 4

dU-CPG 1000
1 µmole columns
0.2 µmole columns

20-2051-01
20-2151-41
20-2151-42

0.1g
Pack of 4
Pack of 4

O

O
N

HN
DMTO

N

N
O

HN
DMTO

O

N
O

O P N(iPr)2

O P N(iPr)22’-deoxyInosine

2’-deoxyUridine

O CNEtO CNEt57

MINOR BASES

The design of primers is frequently complicated by the degeneracy of the genetic code.  Three strategies are now available
to confront this problem.  In the first, a mixed base addition (N) is used to form the degenerate site.  This approach is best
if the number of degenerate sites is small.  A second option is the use of 2’-deoxyInosine or 2’-deoxyNebularine which
exhibit low, but unequal, hydrogen bonding to the other four bases.  The third option is the use of a universal nucleoside.  
In this strategy, the base analog does not hybridize significantly to the other four bases and makes up some of the duplex
destabilization by acting as an intercalating agent.   3-Nitropyrrole 2’-deoxynucleoside (M) is the first example of a setof universal bases.  Subsequently, 5-nitroindole was determined to be an effective universal base and to be superior to
3-nitropyrrole, based on duplex melting experiments.

PCR/SEQUENCING APPLICATIONSDUPLEX EFFECTS (CONT.)OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMade

E
A
M

Item

Catalog No.

Pack

2’-DeoxyNebularine-CE Phosphoramidite(Purine)10-1041-90
10-1041-02

100 µmole
0.25g

5-Nitroindole-CE Phosphoramidite

10-1044-90
10-1044-02

100 µmole
0.25g

dP-CE Phosphoramidite

10-1047-90
10-1047-02

100 µmole
0.25g

dK-CE Phosphoramidite

10-1048-90
10-1048-02

100 µmole
0.25g

dP+dK-CE Phosphoramidite

10-1049-90
10-1049-02

100 µmole
0.25g(Please inquire for availability of vials andcolumns for other instrument types.)

N
N

N
DMTO

N

N
O

58

DMTO

O

N

O P N(iPr)2

O P N(iPr)22’-deoxyNebularine

3-Nitropyrrole

O CNEtNO 2

NO 2

O CNEtDMTONOO P N(iPr)2
O CNEt5-Nitroindole

HN
DMTO

O

MeO

O
Me 2N

N
O

O P N(iPr)2
O CNEt

dP

N
N

HN
N
DMTO

N

N
O

O P N(iPr)2
O CNEtdKPCR/SEQUENCING APPLICATIONSDUPLEX EFFECTS (CONT.)
Unnatural base pairs display unique abilities in duplex DNA and in nucleic acid and protein biosyntheses.   A standard
Watson and Crick base pair is formed between iso-C and iso-G, but the hydrogen bonding pattern is quite different from thenatural base pairs A-T and C-G.  (The 5-methyl analogue was chosen as the synthetic target due to the reported instabilityof 2’-deoxyisocytidine caused by deamination during oligonucleotide synthesis or deprotection.)  
Item

Catalog No.

Pack

dmf-5-Me-isodC-CE Phosphoramidite

10-1065-90
10-1065-02

100 μmole
0.25g

dmf-isodG-CE Phosphoramidite

10-1078-90
10-1078-02

100 μmole
0.25g

RELATED
N4-Et-dC......................................53
N4-Ac-N4-Et-dC..........................53

MINOR BASES

Tm MODULATION
Any technique that involves hybridization of multiple sequences simultaneously, as in DNA chip and reverse hybridization
technologies, is subject to inaccuracies due to differences in GC content. Sequences with high GC content may containmismatches and still hybridize, whereas a low GC content probe may match perfectly and yet disassociate from the target,
leading to false positives and negatives, respectively.
An elegant way of circumventing this problem would be to use a modified base that normalized the stability of the GC andAT base pairs. The N4-ethyl analogue (N4-Et-dC) hybridizes specifically to natural dG but the stability of the base pair isreduced to about the level of an AT base pair. In a series of probes whose GC content ranged from 0 to 100%, the range in
Tm values when N4-Et-dC was used was only 7 °C; when dC was used, that range was 39 °C.

(Me) 2N
DMTO

CH 3

N
N

N
O

O P N(iPr)2
O CNEtdmf-5-Me-isodC

N(Me) 2

N

O

N

N
DPCO
DMTO

N

N
O

O P N(iPr)2
O CNEtdmf-isodG

59

PCR/SEQUENCING APPLICATIONSCLEANAMP® MONOMERSRELATED

CleanAmp® Primers offer an alternative to other Hot Start technologies and allow greater control of primer hybridizationand extension during PCR. It has been demonstrated that CleanAmp® Primers outperform other technologies in multiple
applications. Indeed, over a broad range of applications, CleanAmp® Primers reduce or eliminate off-target amplification.
Greater amplicon yield is also achieved, due to improvement in specificity and sensitivity.  By using either the slow-releasing
Precision primers with two CleanAmp® phosphotriester linkages or the faster-releasing Turbo Primers with a single CleanAmp®
phosphotriester linkage, the rate of formation of unmodified primer can be controlled to suit reaction needs.

UltraMild DNA Synthesis...........27

INTELLECTUAL PROPERTY
CleanAmp® is a trademark of TriLink
BioTechnologies, Inc. CleanAmp®
products or portions thereof arecovered by TriLink pending Patent
Applications, US 2007281308 and
WO2007139723, US Provisional
Patent Application Serial # 61/056,
324 and US Patent 6762298 licensed
from the Department of Healthand Human Services. CleanAmp®
products are sold exclusively for
R & D use by the purchaser. They
may not be resold, distributed or
re-packaged. No license is granted
or implied with the purchase of thisproduct. Amplification methods usedin connection with Polymerase Chain
Reaction (“PCR”) Process are coveredby many patents. It may be necessary
to obtain a separate license forcertain patented applications inwhich the product is used.
CleanAmp® Licenses are available
directly from TriLink BioTechnologies.
www.trilinkbiotech.com

Turbo Primers    

Precision Primers

Fast cycling
Multiplex PCR
Improves amplicon yield
Reduces mis-priming/primer dimer formation

Standard cycling
One-step reverse-transcription PCR
Improved specificity and limit of detection
Greatest reduction in mis-priming/primer dimer formation

Synthesis of CleanAmp® Primers requires the use of UltraMild Chemistry.
CleanAmp® Primers and monomers are available from TriLink BioTechnologies.

O
O

HN
N

DMTO

O

N

N

N

O

P

N(iPr)2

CleanAmp™-Pac-dA

60

O
N

HN

N
H
DMTO

(CH2)9CH3OPO

N(iPr)2

DMTO

O

N

O
O

O

O
(CH2)9CH3

Chemical Formula: C52H73N4O9P
Exact Mass: 928.51
Molecular Weight: 929.13
m/z: 928.51 (100.0%), 929.51 (57.7%), 930.52 (18.0%), 931.52(4.3%), 929.52 (1.2%)
Elemental Analysis: C, 67.22; H, 7.92; N, 6.03; O, 15.50; P, 3.33

CleanAmp™-Ac-dC

HN

N

N

O

O
O

O

N

O

DMTO

O
O

O

NHAc

N

O

P

O

(CH2)9CH3OPO

N(iPr)2

N(iPr)2

CleanAmp™-Pac-dG

CleanAmp™-dT

Chemical Formula: C59H77N6O10P
Exact Mass: 1060.54
Molecular Weight: 1061.25
m/z: 1060.54 (100.0%), 1061.55 (65.1%), 1062.55 (22.9%), 1063.55 (6.0%), 1061.54 (2.2%), 1062.54(1.4%)
Elemental Analysis: C, 66.77; H, 7.31; N, 7.92; O, 15.08; P, 2.92

(CH2)9CH3

PCR/SEQUENCING APPLICATIONSCHAIN TERMINATORSRELATEDIn situations where ligation must be blocked at the 5’ terminus, 5’-OMe-dT may be used.  5’-OMe modification of a strand ofsiRNA using 5’-OMe-T can control guide strand selection and targeting specificity.1  5’-Amino-dT terminates an oligonucleotide
with a 5’-amino group which may be used for attaching a peptide or a PNA sequence.  To avoid polymerase extension at
the 3’ terminus, 2’,3’-dideoxynucleoside and 3’-deoxynucleoside CPGs have proved to be effective.  2’,3’- Phosphoramidites
are designed to be used with the 5’-phosphoramidites and supports.  Since these phosphoramidites have no DMT group,
they are not compatible with purification by the DMT-on technique.  Ion exchange HPLC or PAGE should be used to purify
these dideoxy terminated oligos to ensure that shorter sequences (containing 3’-OH) groups are removed.  (3’-Termination
can also be effected using a 3’-3’ linkage formed using 5’-supports, or 3’-spacer C3 CPG.)  

5’-Phosphoramidites..................38
5’-Supports.................................39
3’-Spacer C3 CPG.......................90

REFERENCE(1) P.Y. Chen, et al., RNA, 2008, 14, 263274..

Catalog No.

Pack

5’-OMe-dT-CE Phosphoramidite

10-1031-90
10-1031-02

100 µmole
0.25g

5’-Amino-dT-CE Phosphoramidite

10-1932-90
10-1932-02

100 µmole
0.25g

3’-dA-CPG
1 µmole columns
0.2 µmole columns

20-2004-01
20-2104-41
20-2104-42

0.1g
Pack of 4
Pack of 4

3’-dC-CPG
1 µmole columns
0.2 µmole columns

20-2064-01
20-2164-41
20-2164-42

0.1g
Pack of 4
Pack of 4

3’-dG-CPG
1 µmole columns
0.2 µmole columns

20-2074-01
20-2174-41
20-2174-42

0.1g
Pack of 4
Pack of 4

3’-dT-CPG
1 µmole columns
0.2 µmole columns

20-2084-01
20-2184-41
20-2184-42

0.1g
Pack of 4
Pack of 4

O
HN
MeO

O

O
CH 3

N
O

O P N(iPr)2
O CNEt5’-OMe-Thymidine

HN
MMTNH

CH 3

N

O
O

O P N(iPr)2
O CNEt5’-Amino-dT

NHBz

NHBz
N

N
DMTO

N

N
O

O succinylCPG

3’-dA-CPG

N
DMTO

O

N

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

O
Me 2N

O
O succinylCPG

3’-dC-CPG

OTHER INSTRUMENT TYPES

O
N

HN
N
DMTO

HN

N

N

DMTO

O
O succinylCPG

3’-dG-CPG

O

CH 3

N
O
O succinylCPG

3’-dT-CPG

61

MINOR BASES

Item

PCR/SEQUENCING APPLICATIONSCHAIN TERMINATORS (CONT.)OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMade

E
A
M

Item

Catalog No.

Pack

2’,3’-ddC-CPG
1 µmole columns
0.2 µmole columns

20-2017-01
20-2117-41
20-2117-42

0.1g
Pack of 4
Pack of 42’,3’-ddA-CE Phosphoramidite

10-7001-90
10-7001-02

100 µmole
0.25g

2’,3’-ddC-CE Phosphoramidite

10-7101-90
10-7101-02

100 µmole
0.25g

2’,3’-ddG-CE Phosphoramidite

10-7201-90
10-7201-02

100 µmole
0.25g

2’,3’-ddT-CE Phosphoramidite

10-7301-90
10-7301-02

100 µmole
0.25g(Please inquire for availability of vials andcolumns for other instrument types.)

N(iBu)2

succinylCPG
NH

O

N

2’,3’-ddC-CPG

62

N

N

O

(iPr)2N P O
CNEt

O

O

N

N

N
DMTO

N(iBu)2NN
O

2’,3’-ddAN(iPr)2N P O
CNEt

O

O

Me 2N
N

O

2’,3’-ddC

N(iPr)2N P O
CNEt

O

O

N

HN

N

N
O

2’,3’-ddG

CH 3

HN(iPr)2N P O
CNEt

O

O

N
O

2’,3’-ddT

STRUCTURAL STUDIESSTRUCTURE/ACTIVITY RELATIONSHIP

Item

Catalog No.

Pack

7-Deaza-dA-CE Phosphoramidite

10-1001-95
10-1001-90
10-1001-02

50 µmole
100 µmole
0.25g

7-Deaza-8-aza-dA-CE Phosphoramidite

10-1083-95
10-1083-90
10-1083-02

50 µmole
100 µmole
0.25g

7-Deaza-dG-CE Phosphoramidite

10-1021-95
10-1021-90
10-1021-02

50 µmole
100 µmole
0.25g

7-Deaza-8-aza-dG-CE Phosphoramidite(PPG)

10-1073-95
10-1073-90
10-1073-02

50 µmole
100 µmole
0.25g

7-Deaza-dX-CE Phosphoramidite

10-1076-95
10-1076-90
10-1076-02

50 µmole
100 µmole
0.25g

3-Deaza-dA-CE Phosphoramidite

10-1088-95
10-1088-90
10-1088-02

50 µmole
100 µmole
0.25g

Me 2N

NHBz
N
DMTO

N

N
O

O P N(iPr)2
O CNEt7-Deaza-2’-deoxyAdenosine

DMTO

O

O

N
N
N

N

N

O
O P N(iPr)2
O CNEt7-Deaza-8-Aza-2’-deoxyAdenosine

Me 2N

HN
N
DMTO

N

N
O

O P N(iPr)2
O CNEt7-Deaza-2’-deoxyGuanosine

Me 2N

DMTO

7-Deaza-dG is unstable to iodineoxidation.  Add  a maximum of 2
times when using iodine oxidationor use 0.5M (10-camphorsulfonyl)oxaziridine (CSO) in anhydrous
acetonitrile and 3 min. oxidation
time. (See Glen Report-Vol.9, No.1,
1996,page 8.)

INTELLECTUAL PROPERTY
The use of PPG is subject toproprietary rights of ELITechGroupand it is sold under license from
ELITechGroup.
(1) I.V. Kutyavin, et al., Nucleic Acids Res.,
2002, 30, 4952-4959.

O

HN
N

STABILITY NOTES

N

N

N

O
O P N(iPr)2
O CNEt7-Deaza-8-Aza-2’-deoxyGuanosine

NHBz

HN
O

N

N
H

DMTO

O
O P N(iPr)2
O CNEt7-deaza-dX

N

N
DMTO

N
O
O P N(iPr)2
O CNEt3-Deaza-dA

63

MINOR BASES

The following products are used to investigate the effect on the activity of an oligonucleotide when key structural elements
are changed.  The 7-deaza purine monomers lack groups critical for hydrogen bonding.  7-Deaza-8-aza-A and 7-deaza-8-aza-G(PPG) monomers are isomers of A and G and have similar electron density.  Their presence in oligos is slightly stabilizing
relative to A and G.  Unlike G, PPG does not lead to aggregation and G-rich oligos can be easily prepared and isolated.  
5’-Fluorescein oligos with PPG at the 5’-terminus are much less quenched than the equivalent G oligos.  As a purine analogueof Thymidine, 7-deaza-2’-deoxyXanthosine (7-deaza-dX) promises to have interesting effects on DNA structure of triplexes.  
7-Deaza-dX also forms a non-standard base pair with a 2,4-diaminopyrimidine nucleoside analogue.  Standard nucleobases
have an unshared pair of electrons that project into the minor groove of duplex DNA.  Enzymes that interact with DNA,
polymerases, reverse transcriptases, restriction enzymes, etc., may use a hydrogen bond donating group to contact thehydrogen bond acceptor in the minor groove.  3-Deaza-2’-deoxyadenosine is very interesting in that it maintains the ability
for regular Watson-Crick hydrogen bonding to T but is lacking the electron pair at the 3-position normally provided by N3.

STRUCTURAL STUDIESSTRUCTURE/ACTIVITY RELATIONSHIP (CONT.)OTHER INSTRUMENT TYPESThe C-nucleoside 2’-deoxypseudouridine, in contrast to dU, forms stable C:pseudoU-A triplets.  2-Aminopurine lacks groups
critical for hydrogen bonding and is a mildly fluorescent base.

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M

Demand for sulfur modified bases continues to expand for investigations of oligonucleotide structure, but primarily forcross-linking purposes.   6-Thio-dG, 4-Thio-dT and 4-thio-dU are very useful modifications for photo cross-linking andphotoaffinity labeling experiments.  Oligos containing 2-thio-dT are useful in examining protein-DNA interaction by acting
as photosensitizing probes.  The thiocarbonyl group in 2-thio-dT is especially interesting in that it is available to react withcompounds associating with the minor groove of DNA.  2-Amino-A forms a very stable base pair with T containing threehydrogen bonds but the stability of the base pair with 2-thio-T is greatly diminished.  Due to steric interactions between
the 2-thio group of thymidine and the 2-amino group of 2-amino-A, the base pair contains only a single hydrogen bond.  
Oligos containing 2-amino-dA and 2-thio-dT exhibit high affinity for natural oligonucleotides but show little affinity for othersimilar oligos even of a complementary sequence.

(Please inquire for availability of vials andcolumns for other instrument types.)

STABILITY NOTES
6-Thio-dG, 4-Thio-dT and 4-thio-dU
are protected as the S-cyanoethyl
ether which is stable during
synthesis and readily removed byammonium hydroxide.  It is criticalto add 50mM sodium hydrosulfide(NaSH) to the ammonium hydroxideused for deprotection.  Especially ifroom temperature deprotection iscarried out, this technique radicallyreduces the level of ammonolysis
which would lead to undesired
aminated bases.  Moreover, it is also
desirable to remove the cyanoethyl
protecting group (1M DBU in
acetonitrile, 2-5 h/RT) prior to theammonium hydroxide cleavage anddeprotection.

Item

Catalog No.

Pack

2’-deoxypseudoU-CE Phosphoramidite

10-1055-95
10-1055-90
10-1055-02

50 µmole
100 µmole
0.25g

2-Aminopurine-CE Phosphoramidite

10-1046-90
10-1046-02

100 µmole
0.25g

6-Thio-dG-CE Phosphoramidite

10-1072-95
10-1072-90
10-1072-02

50 µmole
100 µmole
0.25g

4-Thio-dT-CE Phosphoramidite

10-1034-95
10-1034-90
10-1034-02

50 µmole
100 µmole
0.25g

4-Thio-dU-CE Phosphoramidite

10-1052

Discontinued

2-Thio-dT-CE Phosphoramidite

10-1036-95
10-1036-90
10-1036-02

50 µmole
100 µmole
0.25g

CN

HN
DMTO

NH

O
O
O P N(iPr)2
O CNEt2’-dpseudoU

64

CN

S

O
Me 2N

N

N
N
DMTO

N

N
O

O P N(iPr)2
O CNEt2-Aminopurine

TFAHN
DMTO

S

N

N

O
O P N(iPr)2
O CNEt6-Thio-dG

DMTO

O

O

S

CH 3

N

N

N

CN

N

O P N(iPr)2
O CNEt4-Thio-dT

O

H3C

O

DMTO

O

O

CH 3

N

N
N

DMTO

S

O

N

O P N(iPr)2

O P N(iPr)2

4-Thio-dU

2-Thio-dT

O CNEtO CNEtSTRUCTURAL STUDIESSTRUCTURE/ACTIVITY RELATIONSHIP (CONT.)STABILITY NOTE

2’-DeoxyXanthosine (dX) is a naturally occurring nucleoside that may be derived from oxidative deamination of2’-deoxyGuanosine (dG).  dX has a similar bonding pattern to thymidine and it may base pair with dA, with such purinepurine interactions causing duplex distortion.  dX also featured in attempts to extend the genetic alphabet with a new basepair of dX and pyrimidine-2,4-diamine nucleoside.  dX has also interested researchers in the field of DNA damage and repair
since it is a product of nitric oxide-induced mutagenesis.

Item

Catalog No.

Pack

8-Amino-dA-CE Phosphoramidite

10-1086-95
10-1086-90
10-1086-02

50 µmole
100 µmole
0.25g

8-Amino-dG-CE Phosphoramidite

10-1079 -95
10-1079 -90
10-1079-02

50 μmole
100 μmole
0.25g

2’-dX-CE Phosphoramidite

10-1537-95
10-1537-90
10-1537-02

50 µmole
100 µmole
0.25g

NO2

NMe 2

O

N
N

N

N

N
DMTO

Synthetic oligonucleotides
containing 8-amino-dG must be
cleaved and deprotected withammonium hydroxide containing
0.25M 2-mercaptoethanol to avoid
oxidative degradation of 8-aminodG sites.  

MINOR BASES

8-Amino-dA and 8-amino-dG are useful in triplex formation due to the presence of the additional amino groups.

NOO P N(iPr)2
O CNEt8-Amino-dA

NMe 2(Me 2)N

N

HN
N
DMTO

N

N

N

O
O P N(iPr)2
O CNEt8-Amino-dG

O

N(Me 2)
O2N

N

N
O

N

N

DMTO

O
O

P

N(iPr)2

O

CNEt

dX

65

STRUCTURAL STUDIESHALOGENATED NUCLEOSIDESOTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Brominated and iodinated nucleosides are used in X-ray crystallography studies of oligonucleotide structure.  They are also
photolabile and are used for cross-linking studies to probe the structure of protein-DNA complexes.  Antibodies exist to Br-dU
and oligonucleotides containing Br-dU can be used as probes.  5-Fluoro-dU can be used as a non-photoreactive alternative
to 5-Br-dU with similar electron density.  5-F-dU base pairs more strongly than T to both dA and the dG mismatch.  It is also
useful for probing DNA structure using 19F NMR spectroscopy.

Monomers
For Instrument type

Add

Item

Catalog No.

Pack

Expedite
MerMadeEM

8-Br-dA-CE Phosphoramidite

Columns
For Instrument type10-1007-90
10-1007-02

100 µmole
0.25g

Add

8-Br-dG-CE Phosphoramidite

Expedite
Applied Biosystems 3900
MerMadeEA
M

10-1027-90
10-1027-02

100 µmole
0.25g

5-Br-dC-CE Phosphoramidite

10-1080-90
10-1080-02

100 µmole
0.25g

5-I-dC-CE Phosphoramidite

10-1081-90
10-1081-02

100 µmole
0.25g

5-Br-dU-CE Phosphoramidite

10-1090-90
10-1090-02

100 µmole
0.25g

5-I-dU-CE Phosphoramidite

10-1091-90
10-1091-02

100 µmole
0.25g

5-F-dU-CE Phosphoramidite

10-1092-90
10-1092-02

100 µmole
0.25g

5-Br-dU-CPG
1 µmole columns
0.2 µmole columns

20-2090-01
20-2090-41
20-2090-42

0.1g
Pack of 4
Pack of 4(Please inquire for availability of vials andcolumns for other instrument types.)

STABILITY NOTE
Oligonucleotides containing a
bromo or iodo group are prepared
conventionally with the exceptionthat deprotection is carried out
in ammonium hydroxide at room
temperature for 24 hours.  Under
these conditions, degradation of
the halogen group was less than 2%.

N

N

N

N
DMTO

N

N

CH 3
O

CH 3
Br

Me 2N

N
DMTO

O

O P N(iPr)2ONOO P N(iPr)266

OO CNEt5-Iodo-2’-deoxyCytidine

HN
DMTO

O

DMTO

O

O

N
O

O P N(iPr)2
O CNEt5-Bromo-2’-deoxyUridine

5-Bromo-2’-deoxyCytidine

HN
DMTO

N
O

O CNEtOBrBrO P N(iPr)2

8-Bromo-2’-deoxyGuanosine

NHBz

DMTO

Br

O CNEt8-Bromo-2’-deoxyAdenosine

I

N

N

NHBz
N

O P N(iPr)2

O CNEt

N

N

HN

O

O

I

N
O

O P N(iPr)2
O CNEt5-Iodo-2’-deoxyUridine

HN
DMTO

O

F

N
O

O P N(iPr)2
O CNEt5-Fluoro-2’-deoxyUridine

STRUCTURAL STUDIESDNA DAMAGE/REPAIR

Item

Catalog No.

Pack

8-Oxo-dA-CE Phosphoramidite

10-1008-90
10-1008-02

100 µmole
0.25g

8-Oxo-dG-CE Phosphoramidite

10-1028-95
10-1028-90
10-1028-02

50 µmole
100 µmole
0.25g

5,6-Dihydro-dT-CE Phosphoramidite

10-1530

Discontinued

5,6-Dihydro-dU-CE Phosphoramidite

10-1550-90
10-1550-02

100 µmole
0.25g

5-OH-dC-CE Phosphoramidite

10-1063-90
10-1063-02

100 µmole
0.25g

5-OH-dU-CE Phosphoramidite

10-1053-90
10-1053-02

100 µmole
0.25g

5-Hydroxymethyl-dU-CE Phosphoramidite

10-1093-90
10-1093-02

100 µmole
0.25g

NHBz

O
NH

N

N

N

DMTO

NH

HN

O

iBuHN
DMTO

O

N

N

8-oxo-2’-deoxyAdenosine

8-oxo-2’-deoxyGuanosine

DMTO

O
O

O P N(iPr)2
O CNEt5,6-Dihydro-dU

DMTO

O

N
O

H

O CNEt

O

O

O

OAc
N

O

O P N(iPr)2

O P N(iPr)2

5-OH-dC

5-OH-dU

O CNEtN

5,6-Dihydro-dT

HN
DMTO

5-Hydroxymethyl-dC..................56
dX................................................65

O P N(iPr)2

NH Bz
OBz

RELATEDOO CNEt

N
N

O

DMTO

O P N(iPr)2

HN

Oligonucleotides synthesized using
5,6-dihydro-dU or 5,6-dihydro-dT
and UltraMILD monomers can becleaved using either concentrated
ammonium hydroxide or 50 mM
potassium carbonate in anhydrous
methanol.  Complete cleavage anddeprotection can be accomplishedat room temperature in 2-4 hours
without damaging either thedihydro-dU or dihydro-dT bases.

CH 3

HN

O P N(iPr)2O

Synthetic oligonucleotides
containing 8-oxo-dG must be
cleaved and deprotected withammonium hydroxide containing
0.25M 2-mercaptoethanol to avoid
oxidative degradation of 8-oxo-dG
sites.  

O
OO

O CNEtSTABILITY NOTESO CNEt

HN
DMTO

O

O

OAc
N

O P N(iPr)2
O CNEt5-Hydroxymethyl-dU

67

MINOR BASES

Cellular DNA is constantly being damaged by oxidation and alkylation, by free radicals, and by ultraviolet and ionizing
radiation.   The body has therefore evolved a number of repair enzyme systems to excise and repair these lesions.  
The 8-oxo purine monomers allow investigation of the structure and activity of oligonucleotides containing an 8-oxo mutation
which is formed naturally when DNA is subjected to oxidative conditions or ionizing radiation.  5,6-Dihydro pyrimidines
are naturally occurring compounds that are structural components of alanine transfer RNA.  Dihydrouracil and the hydroxy
pyrimidines are major base damage products formed by exposure of DNA to ionizing radiation.

STRUCTURAL STUDIESDNA DAMAGE/REPAIR (CONT.)STABILITY NOTES
Synthetic oligonucleotides
containing 8-amino-dG must be
cleaved and deprotected withammonium hydroxide containing
0.25M 2-mercaptoethanol to avoid
oxidative degradation of 8-aminodG sites.
Oligonucleotides synthesizedusing Thymidine Glycol andUltraMILD monomers can becleaved using either concentrated
ammonium hydroxide or 50 mM
potassium carbonate in anhydrous
methanol.  Complete cleavage anddeprotection can be accomplishedat room temperature in 2-4 hours
without damaging Thymidine Glycolbase.  The best method to remove
the TBDMS groups was achieved
using TEA.3HF at 40°C overnight.  

REFERENCE

8-Amino-G is formed along with 8-oxo-G as the major mutagenic lesions formed in DNA damage caused by 2-nitropropane.
2-Nitropropane is an industrial solvent and a component of paints, dyes and varnishes, and is also present in cigarettesmoke.   Thymine glycol (5,6-dihydroxy-5,6-dihydrothymine) is formed when thymine is subjected to oxidative stress,
including ionizing radiation.  Oxidation of the 5,6 double bond of Thymidine generates two chiral centers at C5 and C6.  
The cis-5R,6S form is generated as the predominant product along with the other diastereomer, the cis-5S,6R form.  
The presence of thymidine glycol in DNA has significant biological consequences and many organisms possess specificrepair enzymes for the excision of this lesion.  
Hydrolysis of nucleoside residues in DNA occurs to generate abasic sites.  Most commonly, dA sites are hydrolyzed causing
depurination and leading to abasic residues.  For researchers trying to determine if their source of depurination in chemical
synthesis of DNA is reagent, fluidics or protocol-based, we offer a depurination-resistant dA monomer.  A new chemical
method allows the generation of abasic sites in double and single stranded oligonucleotides using very mild specificconditions and with very low probability of side reactions.  Abasic II Phosphoramidite1 has the advantage of simplicity inthat the silyl group is removed post-synthesis using aqueous acetic acid.  dSpacer has also been used successfully as a
mimic of the highly base-labile abasic site.

Item

Catalog No.

Pack

8-Amino-dG-CE Phosphoramidite

10-1079-95
10-1079-90
10-1079-02

50 µmole
100 µmole
0.25g

Thymidine Glycol CE Phosphoramidite

10-1096-95
10-1096-90
10-1096-02

50 µmole
100 µmole
0.25g

Abasic II Phosphoramidite(dR Precursor)

10-1927-95
10-1927-90
10-1927-02

50 µmole
100 µmole
0.25g(1) K. Groebke, and C.J. Leumann, Helv
Chim Acta, 1990, 73, 608-617.

RELATEDdSpacer.......................................90
Pyrrolidine..................................69

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)O(Me 2)N

N

HN
N
DMTO

N

N

N

O
O P N(iPr)2
O CNEt8-Amino-dG

68

O

N(Me 2)
HN
DMTO

O

O

CH 3

OTBDMSNOTBDMSHO P N(iPr)2
O CNEtThymidine Glycol

DMTO

O
OTBDMSOP

N(iPr)2O

CNEt

Abasic II Phosphoramidite

STRUCTURAL STUDIESDNA DAMAGE/REPAIR (CONT.)

Item

Catalog No.

Pack

Cis-syn Thymine Dimer Phosphoramidite

11-1330-95
11-1330-90
11-1330-02

50 µmole
100 µmole
0.25g

5’,8-Cyclo-dA CE Phosphoramidite

10-1098

Discontinued

5’,8-Cyclo-dG CE Phosphoramidite

10-1598

Discontinued

INSTRUMENT TYPESFor these very expensive
phosphoramidites, an ABI septum
vial is the standard vial.  Add E to thecatalog no. for an Expedite vial or V tothe catalog no. for an Expedite V vial.

MINOR BASES

One of the major sources of DNA damage in all organisms is the UV component of sunlight.  The predominant reaction
induced by UV light on DNA is dimerization of adjacent pyrimidine bases leading to cyclobutane dimers (CPDs).  
The dimers formed in the most significant quantity are the cis-syn cyclobutane dimer of two thymine bases.  Although formed
routinely, these dimer products are efficiently excised and repaired enzymatically by nucleotide excision repair (NER) or the
dimerization is reversed by photolase enzymes. A further mode of oxidative damage is radiation-induced damage of DNA,
which has been shown to lead to bridged cyclonucleosides.  The purines, cyclo-dA and cyclo-dG, are predominantly formed,
although the cyclo pyrimidines have also been detected.  Cyclo-dA is doubly intriguing since it contains both damaged
base and damaged sugar residues and, as such, should have a considerable biological impact.  In a manner analogous tothymine dimer, cyclo purines cause significant distortion of the regular DNA helix and these lesions are repaired not bybase excision repair (BER) but by NER.

Base excision repair (BER) is one of the most studied repair mechanisms. In this pathway, DNA glycosylases recognize
the damaged bases and catalyze their excision through hydrolysis of the N-glycosidic bond.  Attempts to understand thestructural basis for DNA damage recognition by DNA glycosylases have been hampered by the short-lived association ofthese enzymes with their DNA substrates. To overcome this problem, the Verdine group at Harvard synthesized a pyrrolidine
analog that mimics the charged transition state of the enzyme-substrate complex.  When incorporated into double-stranded
DNA, they found the pyrrolidine analog (PYR), introduced as the Pyrrolidine-CE Phosphoramidite, forms an extremely
stable complex with the DNA glycosylase AlkA, exhibiting a dissociation constant in the pM range and potently inhibited
the reaction catalyzed by the enzyme.

Item

Catalog No.

Pyrrolidine-CE Phosphoramidite
(PYR)
		

10-1915OO

NO

Discontinued

CH 3

HN
DMTO

Pack

H

O
O P O
OCH 3

O
CH 3

NHBz

NH
H
O

N

O

O P N(iPr)2
OCH 3

Cis-syn Thymine Dimer

N
N

DMTO

O

N
N

N
THPO

N

O
O

NH
N

O

P

N(iPr)2O

CNEt

5’,8-Cyclo-dA

O

O
N
H

O

O
DMTO

N

P

N(iPr)2

P

N(iPr)2

O

CNEt

O

CNEt

5’,8-Cyclo-dG

PyrrolidineO

69

STRUCTURAL STUDIESCLICK DNA AND RNA LIGATION
BIOCOMPATIBLE TRIAZOLE
LINKAGE
DNA
base

O

O

O

DNA

base

O

O

O

+

N3

O

base

N

O
-O

N

base

O

N
O

base

P

O

O

O

O

O

O

DNA

DNA

DNA

RELATED
5’-I-dT in Click Chemistry...........96
Click Chemistry...........................94

REFERENCES - CLICK LIGATION(1) A.H. El-Sagheer, A.P. Sanzone, R. Gao,
A. Tavassoli, and T. Brown, Proc Natl
Acad Sci U S A, 2011, 108, 11338-43.
(2) A.H. el-Sagheer, and T. Brown, Chem
Commun (Camb), 2011, 47, 12057-8.
(3) A.P. Sanzone, A.H. El-Sagheer, T.
Brown, and A. Tavassoli, Nucleic Acids
Res, 2012.
(4) A. Dallmann, et al., Chemistry, 2011,
17, 14714-7.
(5) A.H. El-Sagheer, and T. Brown, Proc
Natl Acad Sci U S A, 2010, 107,
15329-34.

REFERENCES - MicroRNA Labeling(1) H. Vogel, and C. Richert,
ChemBioChem, 2012, 13, 1474-82.
(2) R. Eisenhuth, and C. Richert, Journalof Organic Chemistry, 2008, 74, 2637.
(3) E. Kervio, A. Hochgesand, U.E.
Steiner, and C. Richert, Proc Natl
Acad Sci U S A, 2010, 107, 12074-9.

Ligation of an oligo containing a 5’-azide with an oligo containing a 3’-propargyl group using Click Chemistry leads to atriazole linkage that has been shown to have in vivo biocompatibility.  This technique has been used to synthesize DNA
constructs up to 300 bases in length.  When the resultant triazole linkage was placed in a PCR template, various polymerases
were able to copy the sequence correctly.  The linkage has also been shown to be compatible with transcription and rolling
circle amplification, as well as gene expression in E. coli.  In the RNA world, a hammerhead ribozyme containing the triazole
linkage at the substrate cleavage site has been shown to retain its activity.  A large variety of applications is envisaged forthis biocompatible chemical ligation.  Support for this technology is offered with the help of Tom Brown’s group at the
University of Southampton.
base

Item

Catalog No.

Pack

3’-Propargyl-5-Me-dC CPG

20-2982-01
20-2982-10
20-2982-41
20-2982-42
20-2982-13
20-2982-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)5’-LABELING OF MicroRNAs
Several methods have been developed for the detection of miRNAs, however, few allow the simultaneous detection ofmultiple miRNAs.   To overcome this analytical deficiency, the Richert group at the University of Stuttgart has recently
developed an ingenious method to selectively detect miRNAs on microarrays without interference from endogenous premRNAs, mRNAs and other RNA species.  In this method, a short oligonucleotide containing 3’-amino-dT and a 5’ reportermolecule is chemically ligated to the microRNA in a one-step procedure by in situ activation of the microRNA.  This isspecifically achieved by taking advantage of the fact that miRNAs, unlike other RNAs,  are 5’-phosphorylated. The reaction
is template-directed (and thus sequence specific) and can be performed together with enzymatic 3’-extension/labeling,either in solution or on a support.  The short DNA labeling strand may feature one of a variety of different labels, such asa biotin group or a fluorophore.

Item

Catalog No.

Pack

3’-Amino-dT CPG

20-2981-01
20-2981-10
20-2981-41
20-2981-42
20-2981-13
20-2981-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
O

H
N

O

O

CH3

N
O

DMTO

N

O
O

CH3

HN

NH
O

DMTO

N

O
HN
O

CF2

F2C

CF2

H
N

O

70

3’-Propargyl-5-Me-dC CPG

3’-Amino-dT CPG

STRUCTURAL STUDIES
2’-5’ LINKED OLIGONUCLEOTIDES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Item

Catalog No.

Pack

Columns
For Instrument type

Add

3’-dA-CE Phosphoramidite

10-1004-95
10-1004-90
10-1004-02

50 µmole
100 µmole
0.25g

Expedite
Applied Biosystems 3900
MerMadeE
A
M

3’-dC-CE Phosphoramidite

10-1064-95
10-1064-90
10-1064-02

50 µmole
100 µmole
0.25g

3’-dG-CE Phosphoramidite

10-1074-95
10-1074-90
10-1074-02

50 µmole
100 µmole
0.25g

3’-dT-CE Phosphoramidite

10-1084-95
10-1084-90
10-1084-02

50 µmole
100 µmole
0.25g

3’-dA-CPG
1 µmole columns
0.2 µmole columns

20-2004-01
20-2104-41
20-2104-42

0.1g
Pack of 4
Pack of 4

3’-dC-CPG
1 µmole columns
0.2 µmole columns

20-2064-01
20-2164-41
20-2164-42

0.1g
Pack of 4
Pack of 4

NHBz

NH Bz

N

N
DMTO

OTHER INSTRUMENT TYPES

N

N

N

DMTO

O

O

O

iBuHN
DMTO

N

O P N(iPr)2

O P N(iPr)2

3’-dA

3’-dC

O CNEtO

O CNEt

O

N

HN

N

N

DMTO

O

O P N(iPr)2
O CNEt

3’-dG

CH 3

HN
O

O

DMTO
O P N(iPr)2
O CNEt3’-dT

RELATED
3’-deoxynucleoside CPG............39

NHBz

NHBz
N

N

N

(Please inquire for availability of vials andcolumns for other instrument types.)NNO

O succinylCPG

3’-dA-CPG

N
DMTO

O

N
O
O succinylCPG

3’-dC-CPG

71

MINOR BASES

Cellular DNA and RNA are made up of ribo- and 2’-deoxyribonucleic acids linked together via 3’-5’ phosphodiester linkages
and by far comprise the bulk of polynucleic acids found in cells.  Much less common are oligonucleotides which have 2’-5’linkages.  However, a unique feature of 2’-5’ linked oligonucleotides is their ability to bind selectively to complementary RNA.  
These features suggest a number of interesting uses for 2’-5’ linked oligos such as their use as RNA specific probes
or in antisense oligos.   Recently, oligos have been synthesized using 3’-deoxy-2’-phosphoramidites and 2’-deoxy-3’phosphoramidites to produce  chimeras with 2’-5’ linked ends and 3’-5’ linked central regions.  It was found that 2’-5’phosphorothioate oligos: 1) bind selectively to complementary RNA with the same affinity as phosphodiester oligos;  2) exhibit
much less nonspecific binding to cellular proteins;  3) do not activate RNase H.  A 3’-deoxynucleoside at the 3’-terminus ofan otherwise normal oligonucleotide effectively blocks polymerase extension.

STRUCTURAL STUDIES
2’-5’ LINKED OLIGONUCLEOTIDES (CONT.)
RELATED
N6-Me-dA...................................53

Item

Catalog No.

Pack

3’-dG-CPG
1 µmole columns
0.2 µmole columns

20-2074-01
20-2174-41
20-2174-42

0.1g
Pack of 4
Pack of 4

3’-dT-CPG
1 µmole columns
0.2 µmole columns

20-2084-01
20-2184-41
20-2184-42

0.1g
Pack of 4
Pack of 4

MUTAGENESIS
Cellular polynucleotides are alkylated by endogenous components, such as S-adenosylmethionine, or after reacting with
two general classes of environmental and laboratory chemicals. SN1 chemical agents include alkylnitrosourea and N-alkyl-Nnitro-N-nitrosoguanidine that react with the N7 position of guanine, N3 of adenine, O6 of guanine, O2 or O4 of pyrimidines,
and the non-phosphodiester oxygen atoms of the phosphate backbone.  In contrast, SN2 chemical agents such as methyl
methanesulfonate and dimethyl sulfate react primarily with the N1 position of adenine (1-Methyl-2’-deoxyadenosine) and N3of cytosine.  To avoid chain branching during synthesis when using DCI as activator, N6-Me-dA is offered with acetyl protection.

Item

Catalog No.

Pack

O6-Me-dG-CE Phosphoramidite

10-1070-90
10-1070-02

100 µmole
0.25g

N6-Me-dA-CE Phosphoramidite

10-1003-90
10-1003-02

100 µmole
0.25g

N6-Ac-N6-Me-dA-CE Phosphoramidite

10-1503-90
10-1503-02

100 µmole
0.25g

O4-Me-dT-CE Phosphoramidite

10-1032

Discontinued

1-Me-dA-CE Phosphoramidite

10-1501-95
10-1501-90
10-1501-02

50 µmole
100 µmole
0.25g

O
Me 2N

O
N

HN
N
DMTO

N

N

O

DMTO

O

N
O

O succinylCPG

3’-dG-CPG

OMe
N

N
iBuHN
DMTO

N

N
O

O P N(iPr)2
O CNEt72

O6-Me-2’-deoxyGuanosine

DMTO

O P N(iPr)2
O CNEt

N6-Methyl-2’-deoxyAdenosine

N

N
DMTO

O
O

P

N(iPr)2O

CNEt

N6-Ac-N6-Me-dA

DMTO

O



CH 3

N

N

N

N
O

OMe

NAc

N
N

O succinylCPG

3’-dT-CPG

Me

NHMe
N

CH 3

HN

 

N
O

O P N(iPr)2
O CNEtO4-Me-ThymidineL  

1-Methyl-2’-deoxyAdenosine

STRUCTURAL STUDIESIN SITU SYNTHESIS OF DNA ANALOGSOTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Item

Catalog No.

Pack

Columns
For Instrument type

Add

TMP-F-dU-CE Phosphoramidite(Convertible F-dC)

10-1016-90
10-1016-02

100 µmole
0.25g

Expedite
Applied Biosystems 3900
MerMadeE
AM

O6-Phenyl-dI-CE Phosphoramidite(Convertible dA)

10-1042-90
10-1042-02

100 µmole
0.25g(Please inquire for availability of vials andcolumns for other instrument types.)

O4-Triazolyl-dU-CE Phosphoramidite(Convertible dU)

10-1051-90
10-1051-02

100 µmole
0.25g

2-F-dI-CE Phosphoramidite(Convertible dG)

10-1082-95
10-1082-90
10-1082-02

50 µmole
100 µmole
0.25g

ABBREVIATIONTMP = 2,4,6-trimethylphenyl

NO 2

N
O
F

N
DMTO

O

N
O

O P N(iPr)2
O CNEt

TMP-F-dU

N

OPh
N

N
DMTO

N

N
O

O P N(iPr)2
O CNEtO6-Phenyl-dI

N

O

DMTO

O

N

N

N
N
O
O P N(iPr)2
O CNEtO4-Triaz.-dU

F

DMTO

N

N
O

O P N(iPr)2
O CNEt2-F-dI73

MINOR BASES

The convertible nucleoside strategy is one of the most versatile methods for producing modifications in bases to examine
their effects on DNA structure and activity.  In some cases, with versatility comes difficulty in that the convertible base ismodified after oligonucleotide synthesis.  The chemistry is sometimes complex and base composition analysis of the final
oligonucleotide is required to verify structure.  The convertible dU monomer can be used to introduce a variety of modifications
at the convertible position, including N, O and S modifications.  Convertible F-dC is by far the simplest approach to the
preparation of oligonucleotides containing F-dC - normal ammonium hydroxide treatment effects the conversion to F-dC.  
Convertible dA has been used to prepare oligonucleotides containing multiple points for attachment to solid supports.  In thisway, high capacity affinity supports for the purification of DNA binding proteins have been prepared.  2-F-dI is a convertible
nucleoside for the preparation of 2’-dG derivatives following the displacement of the 2-fluorine by primary amines.

STRUCTURAL STUDIESPROBING DNA STRUCTURE WITH FLUORESCENT NUCLEOSIDESRELATED
2-Aminopurine...........................64
AP-dC (G-Clamp)........................52
UltraMild Chemistry...................27
Pyrrolo-C...................................138
Pyrrolo-CTP...............................142

INTELLECTUAL PROPERTY
Pyrrolo-dC is a joint development
project of Berry & Associates, Inc.
and Glen Research Corporation.  
Pyrrolo-dC is covered by US PatentNo.: 7,144,995.

Etheno-dA is a fluorescent nucleoside which is especially useful in observing the transition between DNA structural types.  
It is quite base labile and should be deprotected with ammonium hydroxide at room temperature for 24 hours.  Alternatively,
UltraMild chemistry can be used.  2-Aminopurine and AP-dC (G-Clamp) are also useful fluorescent nucleosides.
Pyrrolo-dC is a fluorescent deoxycytidine analog that is an ideal probe of DNA structure and dynamics.1,2  It base-pairs as
a normal dC nucleotide.  An oligo fully substituted with pyrrolo-dC has the same Tm as the control dC oligo with the same
specificity for dG.  Its small size does not perturb the structure of the DNA helix and it is well tolerated by a number of
DNA and RNA polymerases.  It is highly fluorescent and its excitation and emission are well to the red of most fluorescentnucleotide analogs, which eliminates or reduces background fluorescence from proteins.  Pyrrolo-dCTP has potential uses
in biological assay development.

Item

Catalog No.

Pack

Etheno-dA-CE Phosphoramidite

10-1006-90
10-1006-02

100 µmole
0.25g

Pyrrolo-dC-CE Phosphoramidite

10-1017-95
10-1017-90
10-1017-02

50 µmole
100 µmole
0.25g

Pyrrolo-dCTP(10 mM)

81-1017

Discontinued

SPECTRAL PROPERTIESThe spectral properties of pyrrolo-dC,
coupled with its unique base-pairing
ability, make this fluorescent analog
extremely valuable in probing DNA
structure.  When the pyrrolo-dC
is base-paired, its fluorescence issignificantly quenched through what
is most likely base stacking or dG
interactions.  The quantum yield of
fluorescence for pyrrolo-dC is quitesensitive to its hybridization state,making it ideally suited for probing
the dynamic structure of DNA.
QY
l
e
			
(L/mol.cm)
single-stranded 0.07 260nm
		 347nm

4000
3700

double-stranded 0.02
(QY determined relative to quinine
sulfate in 0.5M H2SO4)REFERENCES
1. D.A. Berry, et al., Tetrahedron Lett,
2004, 45, 2457-2461.
2. The Glen Report, 2007, 19, 8-9.
3. P. Sandin, et al., Nucleic Acids Res.,
2008, 36, 157-167.
4. P. Sandin, et al., Nucleic Acids Res.,
2005, 33, 5019-5025.
5. K.C. Engman, et al., Nucleic Acids Res.,
2004, 32, 5087-5095.

N

DMTO

N

N
O

O P N(iPr)2
O CNEtEtheno-2’-deoxyAdenosine

74

HN

N

N

HN

N
DMTO

O

O

N

O P N(iPr)2

O

O

O

NaO P O P O P O
ONa

ONa

ONa

O CNEtPyrrolo-dC

N
O

O

OH

Pyrrolo-dCTPN

STRUCTURAL STUDIESPROBING DNA STRUCTURE WITH FLUORESCENT NUCLEOSIDES (CONT.)
SPECTRAL PROPERTIES				
Absorbance Emission
Maximum Maximum
Pyrene-dU
Perylene-dU

Item

Catalog No.

Pack

Pyrene-dU-CE Phosphoramidite

10-1590-95
10-1590-90
10-1590-02

50 µmole
100 µmole
0.25g

10-1591-95
10-1591-90
10-1591-02

50 µmole
100 µmole
0.25g

Perylene-dU-CE Phosphoramidite

402nm
473nm

472nm
490nm

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

O

O

HN
DMTO

HN

N

O

O P N(iPr)2
O CNEtPyrene-dU

N

O
DMTO

O

O

O

P

N(iPr)2O

CNEt

Perylene-dU

75

MINOR BASES

By attaching pyrene or perylene to the 5 position of deoxyuridine through a triple bond, the fluorophore is electronicallycoupled to the deoxyuridine base.   This electronic coupling of the base and the fluorophore makes the fluorescencesensitive to the base pairing of the dU portion of the molecule, allowing the discrimination between perfect and one basemismatched targets.

STRUCTURAL STUDIESPROBING DNA STRUCTURE WITH FLUORESCENT NUCLEOSIDES (CONT.)
RELATED
Ribo-tCo....................................142

SPECTRAL PROPERTIES
Absorption and emission data for tC
and tCo are collected below:
tC
QY
l
e
			
(L/mol.cm)
single-stranded

0.21 385nm

4000

The tricyclic fluorescent nucleoside analogues, 1,3-diaza-2-oxophenothiazine, tC, and 1,3-diaza-2-oxophenoxazine, tCo, aredeoxycytidine analogs that have been shown to base pair faithfully with dG with virtually no disruption of the normal duplex
structure.3-5   This means that the stability of the DNA duplex is not compromised as compared to the control regardlessof DNA sequence.  The fluorescence quantum yield of tC is essentially unchanged between single stranded and double
stranded DNA - 0.21 for single stranded DNA and 0.19 for duplex DNA.  Also, the fluorescence characteristics of tC are notsensitive to neighboring base combinations.  tCo has been shown to be the brightest fluorescent nucleoside analogue induplex context reported so far and even retains the majority of its fluorescence when surrounded by guanine residues.
Indeed, tCo has been reported to be 25-50 times brighter than 2-aminopurine.
The base analogue tCnitro is a FRET-acceptor together with tCO (or tC) as the donor molecule.  This constitutes the first everdescription of a nucleobase FRET-pair.  This novel FRET-pair provides a unique tool for investigations of nucleic acid containing
systems.  tCnitro is virtually non-fluorescent under normal conditions.

double-stranded 0.19
tCo
QY
l
e
			
(L/mol.cm)
single-stranded

0.30 360nm

9000

Item

Catalog No.

Pack

tC-CE Phosphoramidite

10-1516-95
10-1516-90
10-1516-02

50 µmole
100 µmole
0.25g

tC°-CE Phosphoramidite

10-1517-95
10-1517-90
10-1517-02

50 µmole
100 µmole
0.25g

tCnitro-CE Phosphoramidite

10-1518-95
10-1518-90
10-1518-02

50 µmole
100 µmole
0.25g

double-stranded 0.21
(QY determined relative to quinine
sulfate in 0.5M H2SO4)INTELLECTUAL PROPERTY
These products are offered incollaboration with ModyBase HB.

NO2
HN
N

O

P

N(iPr)2

O

CNEt

tC

76

O

P

N(iPr)2

O

CNEt

tCo

N

O
DMTO

O

S

N

N

O
DMTO

O

O

N

N

O
DMTO

HN

HN
S

O

O

P

N(iPr)2O

CNEt

tCnitroSTRUCTURAL STUDIESPHOTO-REGULATION OF DNA FUNCTIONREFERENCES

Glen Research’s interest lies in the preparation of caged oligonucleotides whose function is restored after uncaging by UVlight at a wavelength that causes no DNA damage.  The Deiters group at North Carolina State University has described
NPOM-Caged-dT, where the nucleobase is caged with the photolabile group, 6-nitropiperonyloxymethyl (NPOM), which
can be removed using UV light at 365 nm.  Oligonucleotides containing NPOM-Caged-dT every five or six bases do not
hybridize to their complementary strand.  Photo-uncaging of the caged oligonucleotide is then easily carried out with UVlight at 365 nm for seconds to minutes to restore the activity of the oligonucleotide.

(1) G. Sheikhnejad, et al., J Mol Biol, 1999,
285, 2021-2034.
(2) V.E. Marquez, et al., Antisense Nucleic
Acid Drug D, 1999, 9, 415-421.

RELATED
Convertible F-dC.........................39
5-Fluoro-2’-deoxyUridine..........66
Pyrrolidine..................................69

OTHER INSTRUMENT TYPES
Item

Catalog No.

Pack

DEACM-Caged-dG-CE Phosphoramidite    

10-1533-95
10-1533-90
10-1533-02

50 µmole
100 µmole
0.25g

NPOM-Caged-dT-CE Phosphoramidite    

10-1534-95
10-1534-90
10-1534-02

50 µmole
100 µmole
0.25g

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

CH3

O
H3C

N
N

DMTO

O
O
O

O

O

NO2

P

N(iPr)2O

CNEt

NPOM-Caged-dT

O

DEACM--Caged-dG

77

MINOR BASES

Photocaged oligonucleotides allow for the spatial temporal control of biological processes. In their caged form, theoligonucleotides are unable to participate in base pairing. It is only after exposure to non-invasive light that the native
oligonucleotide is released. DEACM-dG is a convenient way to introduce a photocage at specific positions, and the DEACM
is an effective photocleavable group.

STRUCTURAL STUDIESINHIBITION OF DNA METHYLTRANSFERASESRELATED
7-Deaza-8-Aza2’-deoxyGuanosine....................638-oxo-2’-deoxyGuanosine.........67
7-Deaza-2’-deoxyGuanosine.....63
Abasic II Phosphoramidite.........68
dSpacer.......................................90
8-Amino-dG................................68
8-Amino-dA................................65
6-Thio-dG....................................64
2’-deoxypseudoU-CE
Phosphoramidite........................64
5-Hydroxymethyl-dC..................56

Zebularine (pyrimidin-2-one ribonucleoside) is a cytidine analogue that acts as a DNA demethylase inhibitor, as well as acytidine deaminase inhibitor.  This structure is very active biologically and Zebularine is now used as a potent anti-cancer drug.  
A 2’-deoxynucleoside analogue of Zebularine, 5-methyl-pyrimidin-2-one, 2’-deoxynucleoside, has been used to probe
the initiation of the cellular DNA repair process by making use of its mildly fluorescent properties.  This combination of
biological activity and fluorescence properties would make 5-Me-2'-deoxyZebularine a strong addition to our array of
nucleoside analogues.
Cytosine-5-methyltransferases are found in everything from archaebacteria to mammals and when the regulation ofcytosine-5-methyltransferases goes awry, cancer can result.  The mechanism of action for this family of enzymes involves
attack of a cysteine thiol group on the C6 position of cytosine, leading to a transient dihydrocytosine intermediate, whichthen facilitates the nucleophilic attack by C5 on the activated methyl group of the S-adenosyl-L-methionine cofactor.  As withmany enzymes, the intermediate can be trapped using a suicide substrate and 5-fluoro-cytosine has been used extensively inthis role.  An alternate strategy is to use a transition-state mimic that binds to the active site with high affinity.  An excellent
candidate was found in 5-aza-5,6-dihydrocytosine.  Despite not being covalently bound to the enzyme, it was found1,2 to bea more potent inhibitor of cytosine-5-methyltransferases than 5-fluoro-cytosine.  5-Aza-5,6-dihydro-dC is compatible withstandard oligonucleotide synthesis and deprotection conditions and is an excellent tool for use in methyltransferase research.

Item

Catalog No.

Pack

5-Me-2'-deoxyZebularine-CE Phosphoramidite

10-1061-95
10-1061-90
10-1061-02

50 µmole
100 µmole
0.25g

5-Aza-5,6-dihydro-dC-CE Phosphoramidite

10-1511-95
10-1511-90
10-1511-02

50 µmole
100 µmole
0.25g

LARGE SCALE SYNTHESISThe most common side reaction during deprotection of oligonucleotides on a large scale is the alkylation of dT residuesby acrylonitrile, formed by ß-elimination of the cyanoethyl phosphate protecting groups, to generate N3-cyanoethyl-dT.

Item

Catalog No.

Pack

N3-Cyanoethyl-dT

10-1531-90
10-1531-02

100 µmole
0.25g

O

N
O OAc

O P N(iPr)2
O CNEt

Ara-C

78

N

N

N
DMTO

N

N

NHAc

O
DMTO

O

N
O

O P N(iPr)2
O CNEt

5-Me-2'-deoxyZebularine

DMTO

NH

 NOO P N(iPr)2
O CNEt5-Aza-5,6-Dihydro-dCi  

N3-Cyanoethyl-dT

STRUCTURAL STUDIESNON-CANONICAL STRUCTURES

G-QUADRUPLEX
Oligonucleotide structural analysis has demonstrated that DNA and RNA nucleic acid sequences containing G-tracts separated
by other bases spontaneously fold into G-quadruplex structures.  G-quadruplexes are formed when four adjacent guanine
residues stack in a cyclic Hoogsteen hydrogen-bonding arrangement leading to four-stranded helical structures.  The studyof G-quadruplexes in basic genetic processes is an active area of research in telomerase activity, gene regulation, andfunctional genomics.  Guanine analogues that have different hydrogen bonding characteristics - 7-deaza-8-aza-dG and
7-deaza-dG - have proved useful in analyzing G-quadruplex structures.  Similarly, common DNA lesions - 8-oxo-dG andabasic sites - have been used to investigate their effect on G-quadruplex structure and activity.

REFERENCE(1) J. Carter, The Glen Report, 2015, 27.1,
6-8.

RELATED
2’-F-RNA Phosphoramidites....149
2’-F-Arabinonucleic
Acid (2’-F-ANA).........................150
PC Biotin Phosphoramidite.....106
Cyanine 3 Phosphoramidite....112

MINOR BASES

DNA and RNA structures are defined by Watson-Crick rules of hybridization.  However, a variety of DNA and RNA structures
have been defined which do not rely on simple A-T/U and G-C binding.  Since these structures disobey the Watson-Crickcanon, they are described as non-canonical.  Non-canonical DNA and RNA segments are formed as a result of secondary
structures.  These include G-quadruplexes, triplex forming oligos, hairpins, cruciforms, and i-Motif structures.

TRIPLEX-FORMING OLIGONUCLEOTIDES
Triplex-forming oligonucleotides (TFO) bind in the major groove of duplex DNA in a sequence-specific manner through theformation of non Watson-Crick (Hoogsteen) hydrogen bonds.  The formation of a triplex along the major groove competes
with the binding of transcription factors and other proteins that are necessary for transcription, thereby inhibiting theexpression of particular genes.   A variety of nucleoside analogues have been used in TFO - 8-amino-dG, 8-amino-dA,
6-thio-dG and deoxypseudouridine.

i-MOTIF DNA STRUCTURES
Intercalated Motif (i-Motif) DNA structures may be formed in regions rich in 2’-deoxyCytidine.  Especially at acidic pH, thesestructures could be described as C-Quadruplexes with two parallel stranded sequences also held together in an antiparallelorientation by cytosine-cytosine base pairs.  Since these structures are stable at acidic pH, they can act as nanoswitches bychange in pH.  As they were not considered to be stable at physiological pH, they were not initially considered to be relevant
to biological systems.  However, the stability of the cytosine-cytosine base pair is enhanced by intercallating ligands andso a variety of i-Motif structures are now considered to be biologically significant.  Since i-Motif structures have now been
observed forming and dissolving in living cells, these structures are now the subject of active investigation of the meaningof their activity in human cells.  Research is also being directed to the effect of common DNA lesions, like depurinated sites,
8-oxo-dG and 5-hydroxymethyl-dC, on these transient structures.

APTAMER DEVELOPMENT
Aptamers, generated through repetitive selection using SELEX or an equivalent in vivo procedure, are chosen for theirability to bind desired target molecules, which are frequently small molecules useful in therapeutics.  In some ways, they
may be described as chemically engineered versions of antibodies.  Of course, nucleic acid aptamers have advantages overantibodies in that they can be developed rapidly by in vitro methods, with the reproducibility of chemical synthesis andinherent stability of modified oligonucleotides.  A full battery of base, sugar and internucleotide modifications is available
for aptamer development.
2’-F-RNA has been used extensively in aptamer development, as well as 2’-F-ANA more recently.  An article in The Glen
Report by Jeff Carter, Director, Process Chemistry, SomaLogic, Inc. described1 the use of a DNA backbone with 5-substituteddU analogues as low off-rate modified aptamer (SOMAmer®) reagents to enable multiplexed screening of thousands ofserum or plasma proteins.  These aptamers also include PC Biotin along with a fluorophore, in this case Cyanine 3, forsubsequent detection.  

79

MODIFIERSTERMINUS MODIFIERSINTELLECTUAL PROPERTY
5’-Carboxy-Modifier C10 is offered
for sale under license from TriLink
BioTechnologies, Inc.  It is intended
for research and development
purposes only, and may not be used
for commercial, clinical, diagnostic
or any other use.  It is covered
under US Patent No. 6,320,041.

Glen Research 5’-Modifiers are designed for use in DNA synthesizers to functionalize the 5’-terminus of the target
oligonucleotide.  The 5’-Amino-Modifiers are available with a variety of chain lengths to fit exactly the desired application.
The DMS(O)MT-protected amino group is easier to deprotect compared to the MMT-protected one. The sulfoxy derivative
survives conditions of oligonucleotide synthesis and can either be cleaved with standard deblock solution, or left intact for
HPLC purification. At the same time, the DMS(O)MT group is fully compatible with cartridge purification.  When detritylation
on a cartridge is carried out, the DMS(O)MT+, which is more stable than MMT+, does not reattach itself to an amine.  
We now offer 5’-DMS(O)MT-Amino-Modifier C6 utilizing this new trityl based protecting group.   
5’-Amino-Modifier TEG, a hydrophilic triethylene glycol ethylamine derivative, is 12 atoms in length and fully soluble inaqueous media.   

RELATEDPC modifiers...............................92

Methacrylate C6 Phosphoramidite is a terminus modifier that attaches a methacrylate functional group to an oligonucleotide.
ABBREVIATIONS
CNEt = Cyanoethyl
CPG = Controlled Pore Glass
DMT = 4,4’-Dimethoxytrityl
Fmoc = Fluorenylmethoxycarbonyl
iPr = Isopropyl
MMT = 4-Monomethoxytrityl
T = Trityl
TFA = Trifluroacetyl

Item

Catalog No.

Pack

5’-Amino-Modifier C3-TFA

10-1923-90
10-1923-02

100 µmole
0.25g

5’-Amino-Modifier C610-1906-90
10-1906-02

100 µmole
0.25g

5’-Amino-Modifier C6-TFA

10-1916-90
10-1916-02

100 µmole
0.25g

5’-Amino-Modifier C12

10-1912-90
10-1912-02

100 µmole
0.25g

5’-Amino-Modifier 5

10-1905-90
10-1905-02

100 µmole
0.25g

5’-DMS(O)MT-Amino-Modifier C610-1907-90
10-1907-02

100 µmole
0.25g

5’-Amino-Modifier TEG

10-1917-90
10-1917-02

100 µmole
0.25g

Methacrylate C6 Phosphoramidite

10-1891-90
10-1891-02

100 µmole
0.25g

TFANH

MMTNH

O P N(iPr)2O P

O CNEtTFANH

N(iPr)2

5’-Amino-Modifier C3-TFA

5’-Amino-Modifier C6-TFA

5’-Amino-Modifier C6

MMTNH

O P N(iPr)2

MMTNH

O CNEt5’-Amino-Modifier C12

O P N(iPr)2
O CNEtO CNEtO

O P N(iPr)2
O CNEt5’-Amino-Modifier 5


H
N

F3C

O

O

O

O

P

N(iPr)2O

CNEt

5’-Amino-Modifier TEG
H
N

80

O

O



 

i 

O

P

N(iPr)2

O CNEtMethacrylate C6 Phosphoramidite

5’-DMS(O)MT-Amino-Modifier C6

MODIFIERSTERMINUS MODIFIERS (CONT.)

Item

Catalog No.

Pack

Universal Phosphoramidite

10-5000-90
10-5000-02

100 µmole
0.25g

Our more recent 5’-amino modifiers, protected by a novel phthalic acid diamide (PDA) protecting group, are stable solids.
In contrast to the TFA protected amino modifiers, which are viscous oils, the analogous PDA protected compounds are
granular powders. This important property of these compounds allows straightforward handling, storage and aliquoting
and leads to a significant increase in stability.  
Deprotection with methylamine in gas phase or aqueous solution or AMA leads to fast and complete removal of the PDA
protecting group. However, ammonium hydroxide will not drive the equilibrium reaction to completion and only partial
deprotection occurs - overnight deprotection with ammonium hydroxide will yield around 80% active amine.
We are offering three PDA Amino-Modifiers:

INTELLECTUAL PROPERTYPDA amino-modifiers were developedby Stefan Pitsch and ReseaChem
GmbH (S. Berger), and covered by
Patent US9534003B2.

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)• 5’-Amino-Modifier C6-PDA• Hydrophobic 5’-Amino-Modifier C12-PDA• Hydrophilic 5’-Amino-Modifier-TEG-PDA

Item

Catalog No.

Pack

5’-Amino-Modifier C6-PDA

10-1947-90
10-1947-02

100 µmole
0.25g

5’-Amino-Modifier C12-PDA

10-1948-90
10-1948-02

100 µmole
0.25g

5’-Amino-Modifier-TEG-PDA

10-1949-90
10-1949-02

100 µmole
0.25g
HN
O
H
N
O

Universal Phosphoramidite
HN

5’-Amino-Modifier C6-PDA

P

N(iPr)2

O

CNEt

HN
O
H
N

O

O

O

5’-Amino-Modifier C12-PDA

P

N(iPr)2

O

CNEt

O
H
N
O

O

O

O

O

P

N(iPr)2O

CNEt

5’-Amino-Modifier-TEG-PDA

81

MODIFICATION/LABELING

Cleavable linkers have a wide range of application uses. We now offer Universal-CE, a dual-purpose linker capable of revealing
3’-OH termini or serving as a 5’-amino modifier C3 upon cleavage. Used as a universal phosphoramidite, the resulting
oligonucleotides with a 3’-OH may be crucial for downstream applications, such as primer extension or ligation assays. Usedas an amino modifier, the resulting oligonucleotides would be identical to those generated with 5’-Amino-Modifier C3-TFA.

MODIFIERSTERMINUS MODIFIERS (CONT.)OTHER INSTRUMENT TYPESThe disulfide thiol modifier may be used for introducing 3’- or 5’-thiol linkages.  Dithiol Serinol, produced from lipoic acidand our patented serinol backbone, allows easy connection of multiply dithiol-labeled oligos to gold surfaces.  5’-CarboxyModifier C10 is a unique linker designed to be added at the terminus of an oligonucleotide synthesis.  It generates anactivated carboxylic acid N-hydroxysuccinimide (NHS) ester suitable for immediate conjugation on the synthesis column
with molecules containing a primary amine, resulting in a stable amide linkage.  An alternative carboxylate protecting groupis the 2-chlorotrityl group, which is simply removed using the standard deblock cycle to generate a free carboxyl groupon an otherwise fully protected oligonucleotide. The 2-chlorotrityl group is also removed during oligo deprotection withammonium hydroxide or AMA and is incompatible with RP purification techniques.  PC Amino-Modifier is a photocleavable
C6 amino-modifier, part of our line of photocleavable (PC) modifiers.  5’-AminoOxy-Modifier 11 is based on a tetraethylene
glycol linkage for improved solubility and for reducing the potential negative impact on hybridization of the oligo.  The oxime
formed from the reaction of alkyloxyamines with aldehydes creates a stable covalent bond.  In comparison, the imine formedby the conjugation of primary amines with aldehydes is not stable to acidic or basic conditions and requires subsequent
reduction with borohydride to form stable amine conjugates.   5’-Maleimide Modifier Phosphoramidite, developed at the
University of Barcelona, incorporates a maleimide cycloadduct that is stable to ammonium hydroxide at room temperature.
This phosphoramidite can be incorporated into DNA and RNA with both phosphate and phosphorothioate linkages.  
A retro–Diels-Alder reaction deprotects the maleimide immediately prior to conjugation.

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

Item

Catalog No.

Pack

5’-Thiol-Modifier C610-1926-90
10-1926-02

100 µmole
0.25g

Thiol-Modifier C6 S-S

10-1936-90
10-1936-02

100 µmole
0.25g

Dithiol Serinol Phosphoramidite

10-1991-95
10-1991-90
10-1991-02

50 µmole
100 µmole
0.25g

PC Amino-Modifier Phosphoramidite

10-4906-90
10-4906-02

100 µmole
0.25g

5’-Carboxy-Modifier C10

10-1935-90
10-1935-02

100 µmole
0.25g

5’-Carboxy-Modifier C510-1945-90
10-1945-02

100 µmole
0.25g

5’-AminoOxy-Modifier 1110-1919-95
10-1919-90
10-1919-02

50 µmole
100 µmole
0.25g

5’-Maleimide-Modifier Phosphoramidite  10-1938-90
10-1938-02

100 µmole
0.25g

Maleimide NHS Ester (SMCC)

50-1938-23

INTELLECTUAL PROPERTY
5’-Maleimide Modifier
Phosphoramidite is protected by apatent application and is offered by
Glen Research under a non-exclusive
license agreement from the Universityof Barcelona.

TS

O P

N(iPr)2DMTO

SO CNEt5’-Thiol-Modifier C6

O

Thiol-Modifier C6 S-S
H3C

O

TFAHN

S

NH

O P N(iPr)2
NO 2

SO CNEt82

O

O P N(iPr)2

5’-Carboxy-Modifier C10

O

S

H
N
O

O

O

O CNEt

Cl

O

O

O

5’-AminoOxy-Modifier 11
H
N

O

O

O

P

N(iPr)2O

CNEt

5’-Carboxy-Modifier C5P

N(iPr)2

O

CNEt

ODMT
O

P

N(iPr)2OO

O-CNEtOOO

N(iPr)2

H
N

OCNEt

Dithiol Serinol

PC Amino-ModifierNP

3.3 mgDMT

H

N

CH2CH2O P

N(iPr)2

H O

O

CNEt

5’-Maleimide-Modifier

Maleimide NHS Ester (SMCC)

MODIFIERS
SEQUENCE MODIFIERS

Item

Catalog No.

Pack

Amino-Modifier C6 dA

10-1089-90
10-1089-02

100 µmole
0.25g

Amino-Modifier C6 dC

10-1019-90
10-1019-02

100 µmole
0.25g

N2-Amino-Modifier C6 dG

10-1529-95
10-1529-90
10-1529-02

50 µmole
100 µmole
0.25g

Carboxy-dT

10-1035-90
10-1035-02

100 µmole
0.25g

Amino-Modifier C2 dT

10-1037-90
10-1037-02
10-1037-05

100 µmole
0.25g
0.5g

Amino-Modifier C6 dT

10-1039-90
10-1039-02
10-1039-05

100 µmole
0.25g
0.5g

N(CH 3)2
NHBz

DMTO

O

N

N
N

N

DMTO

O

O

DMTO

O

O
OMe

N
O

O P N(iPr)2
O CNEtCarboxy-dT

O

HN
DMTO

O

O

O
NH

N
O

O P N(iPr)2
O CNEtAmino-Modifier C2 dT

P

N(iPr)2O

CNEt

N2-Amino-Modifier C6 dG

Amino-Modifier C6 dC

O

N

N

O

N(iPr)2

Amino-Modifier C6 dA

HN

N
H
DMTO

O CNEtO CNEtO

N

HN

CF3CNHN

Amino-Modifier supports..........85

O
O

O

O P

N(iPr)2O P

O
NHCCF 3NH

N

NHCCF 3NHO

N

RELATED

MODIFICATION/LABELING

Sequence Modifiers are designed for use in automated synthesis.   The carboxy-dT is hydrolyzed during deprotection and canbe coupled directly to a molecule containing a primary amino group by a standard peptide coupling or via the intermediate
N-hydroxysuccinimide (NHS) ester.   Amino-Modifier dA, Amino-Modifier dC, N2-Amino-Modifier dG and both AminoModifier dT products can be added in place of a dA, dC, dG and dT residue, respectively, during oligonucleotide synthesis.  
Corresponding Amino-Modifier supports can replace their respective deoxynucleoside supports.  After deprotection, theprimary amine on the C6 analogues is separated from the oligonucleotide by a spacer arm with a total of 7 -10 atoms andcan be labeled or attached to an enzyme.  The C2 analogue is more suitable for the attachment of molecules designed toreact with the oligonucleotide.

O

NHCCF 3

HN
DMTO

O

O

O
NH

NHCCF 3NO

O P N(iPr)2
O CNEtAmino-Modifier C6 dT

83

MODIFIERS
SEQUENCE MODIFIERS (CONT.)
RELATED
Carboxy-Modifiers......................82

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

Our repertoire of NHS ester derivatives has been expanded to include the NHS-Carboxy-dT-CE Phosphoramidite.  By making
a dT analog of the Carboxy-Modifier C10, it is possible to label one or multiple sites within an oligonucleotide.  This opens
up the possibility to label any number of different dyes or molecules within an oligonucleotide when the phosphoramidite
is unavailable.  Doing so is straightforward and may be done manually off the synthesizer or even in a fully-automatedmanner on the DNA synthesizer.
We have never found conditions which allow the TFA group to be removed from an amino-modifier while the oligonucleotide
remains attached to the support.  We are able to solve this problem by using a 9-fluorenylmethoxycarbonyl (Fmoc) protecting
group.  The Fmoc group is removed using a two step procedure, the first to remove the cyanoethyl protection groups andflush the formed acrylonitrile from the synthesis column using 1% diisopropylamine in acetonitrile, and the second to remove
the Fmoc group using 10% piperidine in DMF.  The amino group so formed on the column can be reacted with a variety ofactivated esters.  We offer Fmoc-Amino-Modifier C6 dT Phosphoramidite as a nucleosidic option and Amino-Modifier Serinol
Phosphoramidite as a non-nucleosidic alternative.  We also offer S-Bz-Thiol-Modifier C6-dT to join the ranks of thiol-modifiers
for oligonucleotide synthesis.  Thiol-Modifier C6-dT can be added as usual at the desired locations within a sequence.
Item

Catalog No.

Pack

NHS-Carboxy-dT

10-1535-90
10-1535-02

100 µmole
0.25g

Fmoc-Amino-Modifier C6 dT

10-1536-90
10-1536-02

100 µmole
0.25g

S-Bz-Thiol-Modifier C6-dT

10-1538-95
10-1538-90
10-1538-02

50 µmole
100 µmole
0.25g

Amino-Modifier Serinol Phosphoramidite

10-1997-95
10-1997-90
10-1997-02

50 µmole
100 µmole
0.25g

O

O
HN



O

O

i 
 

NHS-Carboxy-dT
O

84

O

CNEt

H
N

SBz
O
Fmoc

O

O

N(iPr)2

N

O
DMTO

P
O

Fmoc-Amino-Modifier C6 dT

N
H

HN

H
N

H
N
O

P

N(iPr)2

O

CNEt

O
O

N

O
DMTO

 

H
N

N
H

S-Bz-Thiol-Modifier C6-dT

ODMT
O

P

N(iPr)2O

CNEt

Amino-Modifier Serinol Phosphoramidite

MODIFIERS
3’-MODIFIERS
3’-Amino-Modifier CPGs, containing amino groups protected with the base-labile Fmoc group, are designed to functionalize
the 3’-terminus of the target oligonucleotide by the introduction of a primary amine.  In an alternative approach, the nitrogendestined to become the 3’-amino group is included in a phthalimide (PT) group which is attached to the support through anamide group attached to the aromatic ring.  This simple linkage is very stable to all conditions of oligonucleotide synthesis
and contains no chiral center.  Using an extended ammonium hydroxide treatment (55°C for 17 hours), the cleavage of theamine from the phthalimide is accomplished along with the deprotection of the oligonucleotide.  ABI-style columns aresupplied unless otherwise requested.  
Cat. No.

3’-Amino-Modifier C7 CPG 1000

20-2958-01
20-2958-10
20-2958-41
20-2958-42
20-2958-13
20-2958-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2997-01
20-2997-10
20-2997-42
20-2997-41
20-2997-13
20-2997-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2954-01
20-2954-10
20-2954-41
20-2954-42
20-2954-13
20-2954-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2956-01
20-2956-10
20-2956-41
20-2956-42
20-2956-13
20-2956-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

26-2956-01
26-2956-10
26-2956-52
26-2956-55

0.1g
1.0g
Pack of 10
Pack of 10

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3’-Amino-Modifier Serinol CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3’-PT-Amino-Modifier C3 CPG
1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3’-PT-Amino-Modifier C6 CPG
1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
3'-PT-Amino-Modifier C6 PS
200 nmole columns (ABI 3900)
40 nmole columns (ABI 3900)

Pack

O

O
FmocNHODMTO-succinyl-lcaa-CPG

3’-Amino-Modifier C7 CPG

CPG

N

NH
O

MODIFICATION/LABELING

Item

O

3’-PT Amino-Modifier C3 CPG

ODMT

CPG

N

NH
O

O

3’-PT Amino-Modifier C6 CPG

ODMT
Fmoc

H
N

H
N
O

ODMT
O-succinyl-CPG

3’-Amino-Modifier Serinol CPG

85

MODIFIERS
3’-MODIFIERS (CONT.)
RELATED
Dithiol Serinol.............................82

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

The 3’-Thiol-Modifier S-S CPG supports are used to introduce 3’-thiol linkages with three and six atom spacers into
oligonucleotides.  3’-Dithiol Serinol CPG is used to introduce a dithiol group at the 3’-terminus.  In conjunction with Dithiol
Serinol Phosphoramidite, it is simple to produce oligonucleotides with multiple thiol groups at the 3’ terminus, which isideal for conjugation to gold surfaces.  With Glyceryl CPG the 3’-terminus of an oligonucleotide is readily oxidized by sodium
periodate to form a 3’-phosphoglycaldehyde.  The aldehyde may be further oxidized to the corresponding carboxylic acid.  
Either the aldehyde or the carboxylate may be used for subsequent conjugation to amine-containing products.  
Item

Cat. No.

3’-Thiol-Modifier C3 S-S CPG

20-2933-01
20-2933-10
20-2933-42
20-2933-41
20-2933-13
20-2933-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2938-01
20-2938-10
20-2938-42
20-2938-41
20-2938-13
20-2938-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2991-01
20-2991-10
20-2991-42
20-2991-41
20-2991-13
20-2991-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2902-01
20-2902-10
20-2902-42
20-2902-41
20-2902-13
20-2902-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3’-Thiol-Modifier 6 S-S CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3’-Dithiol Serinol CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
3’-Glyceryl CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

DMTO

S

S

O-succinyl-lcaa-CPG

H
N

H
N
S

O

O

3’-Dithiol Serinol CPG

86

O

S

S

O

3’-Thiol-Modifier 6 S-S CPG

3’-Thiol-Modifier C3 S-S CPG

S

DMTO

Pack

ODMT
O

succinoyl-CPG

CPG

O

NH

O
O

ODMT
OAc

3’-Glyceryl CPG

O-succinyl-CPG

MODIFIERS
3’-MODIFIERS (CONT.)
3’-Amino-Modifier C6 dC CPG and 3’-Amino-Modifier C6 dT CPG replace a dC and T, respectively, at the 3’-terminus.  
These products allow convenient labeling at the 3’ without blocking the terminus from desired enzymatic activity.

Item

Cat. No.

Pack

3’-Amino-Modifier C6 dC CPG

20-2019

Discontinued

3’-Amino-Modifier C6 dT CPG

20-2039-01
20-2039-10
20-2039-41
20-2039-42
20-2039-13
20-2039-14

MODIFICATION/LABELING

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

N(CH 3)2
N

O

N
DMTO

O
O

O

O
NH

N

NHCCF 3

O

HN
DMTO

O

O
NH

NHCCF 3NO

O succinyl-lcaa-CPG

O succinyl-lcaa-CPG

Amino-Modifier C6 dC CPG

Amino-Modifier C6 dT CPG

87

MODIFIERS
CHEMICAL PHOSPHORYLATIONINTELLECTUAL PROPERTY

Chemical Phosphorylation Reagent is most commonly used to phosphorylate the 5’-terminus of an oligonucleotide.  
Although this product is also successful in 3’-phosphorylation,  3’-Phosphate CPG allows direct preparation of oligonucleotides
with a 3’-phosphate group.  Chemical Phosphorylation Reagent II contains a DMT group on a side chain which is stable tobase cleavage and can be left on the oligonucleotide for use in RP purification.  The DMT group is later removed with aqueousacid and the side chain is eliminated after brief treatment with aqueous ammonium hydroxide to yield the 5’-phosphate.1
Solid CPR II is similar in performance to CPR II but it is easier to prepare aliquots since it is a powder.  Many researchers treat
synthesis supports with a hindered base (e.g., diethylamine, diisopropylethylamine, or DBU) post-synthesis to eliminate
and remove the cyanoethyl phosphate groups.  In this way, the acrylonitrile formed in situ is removed from the supportand is not available to alkylate dT residues at the N3 position in the oligos.  Since the sulfonylethyl group in 3’-Phosphate
CPG is also susceptible to ß-elimination leading to oligo cleavage, this technique is not compatible with 3’-phosphate CPG.  
Using CPR II CPG, which is base labile but does not support ß-elimination, the cyanoethyl groups can be removed fromthe oligo prior to cleavage and base deprotection.  ABI-style vials and columns are supplied unless otherwise requested.

Solid Chemical Phosphorylation
Reagent II and related supports
are covered by European Patent:
EP0816368.
(1) A. Guzaev, H.Salo, A. Azhayev, and
H. Lonnberg, Tetrahedron, 1995, 51,
9375-9384.

RELATED
High load supports.....................33

Item

Cat. No.

Chemical Phosphorylation Reagent

10-1900-90
10-1900-02

100 µmole
0.25g

3’-Phosphate CPG

20-2900-01
20-2900-10
20-2900-41
20-2900-42
20-2900-13
20-2900-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

26-2900-01
26-2900-10
26-2900-52
26-2900-55
25-2900-01
25-2900-10
25-2900-46

0.1g
1.0g
Pack of 10
Pack of 10
0.1g
1.0g
Pack of 4

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3'-Phosphate PS
200 nmole columns (ABI 3900)
40 nmole columns (ABI 3900)
3’-Phosphate CPG(High Load)
2.5 µmole columns

DMTO
O

S

O P
O

N(iPr)2DMTO

O CNEtOS

MeHNOCO -succinyl-lcaa-CPG

DMTO

O

3’-Phosphate CPG

Chemical Phosphorylation Reagent

EtO2C CO 2Et
O P
DMTO

Chemical Phosphorylation Reagent II

CONHMeO

P

N(iPr)2O

CNEt

Solid Chemical Phosphorylation Reagent II

MeHNOC
N(iPr)2

O CNEt

88

Pack

DMTO

CONHMeO

3’-CPR II CPG

succinyl-CPG

MODIFIERS
CHEMICAL PHOSPHORYLATION (CONT.)
Cat. No.

Chemical Phosphorylation Reagent II(CPR II)

10-1901-90
10-1901-02

100 µmole
0.25g

Solid Chemical Phosphorylation Reagent II(Solid CPR II)

10-1902-90
10-1902-02

100 µmole
0.25g

3’-CPR II CPG

20-2903-01
20-2903-10
20-2903-42
20-2903-41
20-2903-13
20-2903-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)Pack

ALDEHYDE MODIFICATION
Aldehyde modifiers would be attractive electrophilic substitutions in oligonucleotides since they are able to react with aminogroups to form a Schiff’s base, with hydrazino groups to form hydrazones, and with semicarbazides to form semi-carbazones.  
The Schiff’s base is unstable and must be reduced with sodium borohydride to form a stable linkage but hydrazones andsemicarbazides are very stable linkages.
Our collaboration with ELITechGroup, formerly Epoch Biosciences, has allowed us to offer 5'-Aldehyde-Modifier C2
Phosphoramidite.  The acetal protecting group is sufficiently hydrophobic for use in RP HPLC and cartridge purification andis readily removed after oligonucleotide synthesis under standard oligonucleotide detritylation conditions with 80% acetic
acid / 20% water or 2% aqueous trifluoroacetic acid during cartridge purification.

INTELLECTUAL PROPERTY
These Products are for research
purposes only, and may not be used
for commercial, clinical, diagnostic
or any other use. These Products
are subject to proprietary rights of
ELITechGroup and are made and soldunder license from ELITechGroup.
There is no implied license forcommercial use with respect tothese Products and a license must be
obtained directly from ELITechGroup
with respect to any proposedcommercial use of these Products.
“Commercial use” includes but is not
limited to the sale, lease, license orother transfer of the Product or any
material derived or produced from it,
the sale, lease, license or other grantof rights to use the Product or any
material derived or produced from it,or the use of the Product to perform
services for a fee for third parties(including contract research).
A simple agreement must be signed
before end-users and custom
oligo services may purchase theseproducts for use as defined above.  
https://www.glenresearch.
com/media/productattach/
import/technical_note/
ELITechGroupProducts.pdf

OTHER INSTRUMENT TYPES

A formylindole nucleoside analogue has been used to introduce aldehyde groups within an oligonucleotide or at the
5’ terminus.   This product has no protecting group on the aldehyde, which means that deprotection of the modified
oligonucleotide can be done without changing preferred conditions.

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

ItemCat. No.

Monomers
For Instrument type

Add

5'-Aldehyde-Modifier C2 Phosphoramidite

10-1933-90
10-1933-02

100 µmole
0.25g

Expedite
MerMadeE
M

Formylindole CE Phosphoramidite

10-1934-90
10-1934-02

100 µmole
0.25g

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMade

E
A
M

Pack

CHO

(Please inquire for availability of vials andcolumns for other instrument types.)

N
O
O

DMTO
O

O P N
O
CH 2CH 2CN

5'-Aldehyde-Modifier C2OOP

N(iPr)2O

CNEt

Formylindole

89

MODIFICATION/LABELING

Item

MODIFIERSSPACER MODIFIERS
RELATEDThe spacer phosphoramidites C3, 9, C12 and 18 are used to insert a spacer arm in an oligonucleotide.  The compounds may
be added in multiple additions when a longer spacer is required.  3’-Spacer C3 CPG may also act as a blocker of exonucleaseand polymerase activity at the 3’-terminus.  dSpacer is used to introduce a stable abasic site within an oligonucleotide.  
PC Spacer is a photocleavable C3 spacer modifier, part of our line of photocleavable (PC) modifiers.

PC Modifiers...............................92
Pyrrolidine..................................69

Item

Cat. No.

Spacer Phosphoramidite 9

10-1909-90
10-1909-02

100 µmole
0.25g

Spacer Phosphoramidite C3

10-1913-90
10-1913-02

100 µmole
0.25g

dSpacer CE Phosphoramidite

10-1914-90
10-1914-02

100 µmole
0.25g

dSpacer-5'-CE Phosphoramidite

10-4191-90
10-4191-02

100 µmole
0.25g

Spacer Phosphoramidite 18

10-1918-90
10-1918-02

100 µmole
0.25g

Spacer C12 CE Phosphoramidite

10-1928-90
10-1928-02

100 µmole
0.25g

3’-Spacer C3 CPG

20-2913-01
20-2913-10
20-2913-41
20-2913-42
20-2913-13
20-2913-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

10-4913-90
10-4913-02

100 µmole
0.25g

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
PC Spacer Phosphoramidite

Pack

DMTO

DMTO

O

O

O P N(iPr)2DMTO

O P N(iPr)2

O CNEtO P N(iPr)2

O CNEtO CNEtSpacer C3

Spacer 9

O

dSpacer-5'-CE

dSpacer

H3C
DMTO

O

O

O

Spacer 18

90

O

O

O P N(iPr)2DMTO

O P N(iPr)2
O CNEtO CNEtSpacer C12

DMTO

O
NH

PC SpacerO P N(iPr)2
NO 2

O CNEtMODIFIERS
DENDRIMERS

Item

Catalog No.

Pack

Symmetric Doubler Phosphoramidite

10-1920-90
10-1920-02

100 µmole
0.25g

Asymmetric Doubler (LEV) Phosphoramidite

10-1981-90
10-1981-02

100 µmole
0.25g

Trebler Phosphoramidite

10-1922-90
10-1922-02

100 µmole
0.25g

10-1925-90
10-1925-02

100 µmole
0.25g

Long Trebler Phosphoramidite

BRANCHING PHOSPHORAMIDITE
A branching monomer is  required to construct comb-like oligonucleotide probes.  The developers of the comb system from
Chiron Corporation evaluated3 several protecting groups for the branch point and chose levulinyl (LEV), which is specificallyremoved using a reagent containing hydrazine hydrate, acetic acid and pyridine.

Item

Catalog No.

Pack

5-Me-dC Brancher Phosphoramidite

10-1018-90
10-1018-02

100 µmole
0.25g

O

DMTO

O

O P N(iPr)2
NH

O
NH

P

N(iPr)2

O

CNEt

O

DMTO

CH 3

N



DMTO

O

E
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

REFERENCES(1) M.S. Shchepinov, I.A. Udalova, A.J.
Bridgman, and E.M. Southern,
Nucleic Acids Res, 1997, 25, 44474454.
(2) M.S. Shchepinov, K.U. Mir, J.K.
Elder, M.D. Frank-Kamenetskii, andE.M. Southern, Nucleic Acids Res,
1999, 27, 3035-41.
(3) T. Horn, C.A. Chang, and M.S.
Urdea, Nucleic Acids Res, 1997, 25,4842-4849.

O

O

NH

Asymmetric Doubler (LEV)

Add

Expedite
MerMadeO CNEtTrebler

DMTO

Symmetric Doubler

Monomers
For Instrument type

N(iPr)2O P

OOAll minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

O

DMTO

NH
O

O CNEt

O

DMTO

DMTO

O
O

NH

OTHER INSTRUMENT TYPESONOi O P N(iPr)2
O CNEtLong Trebler

5-Me-dC Brancher

91

MODIFICATION/LABELING

Dendrimers are discrete, highly branched, monodispersed polymers that possess patterns reminiscent of the branching oftrees.  Plain and mixed oligonucleotide dendrimers can be synthesized using novel doubling and trebling phosphoramidite
synthons.1,2  Dendrimers offer the following advantages.  Incorporation of label using γ-32P-ATP and polynucleotide kinase
increases in proportion to the number of 5’-ends.  Fluorescent signal also increases in proportion to the number of 5’-ends,
if spacers are incorporated between the labels and the ends of the branches.  When using a dendrimeric oligonucleotide
as a PCR primer, the strand bearing the dendrimer is resistant to degradation by T7 Gene 6 exonuclease making it easy
to convert the double-stranded product of the PCR to a multiply labeled, single-stranded probe.  Enhanced stability of
DNA dendrimers makes them useful as building blocks for the ‘bottom up’ approach to nano-assembly.  These features
also suggest applications in DNA chip technology when higher temperatures are required, for example, to melt secondary
structure in the target.

MODIFIERS
PHOTOCLEAVABLE MONOMERSOTHER INSTRUMENT TYPESPC Biotin Phosphoramidite can be used to prepare 5’-biotinylated oligonucleotides suitable for capture by streptavidin in amode similar to our popular 5’ Biotin Phosphoramidite.   Amino- and thiol-modified oligonucleotides have proven to be very
useful for the attachment of a variety of haptens and fluorophores, as well as for the tethering of the oligonucleotides to adiversity of beads and surfaces.   PC Amino-Modifier Phosphoramidite is used to prepare 5’-amino-modified oligonucleotides
suitable for subsequent photocleavage.  PC Spacer Phosphoramidite can be used as an intermediary to attach any modification
reagent, available as a phosphoramidite, to the terminus of oligonucleotides.   After photocleavage, a 5’-phosphate is
generated on the DNA, rendering it suitable for further biological transformations, such as gene construction and cloning
after ligation.

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeEA
M

A versatile photocleavable DNA building block has been described by researchers in Washington University, Missouri andused in phototriggered hybridization.1  This reagent has also been used in the design of multifunctional DNA and RNA
conjugates2 for the in vitro selection of new molecules catalyzing biomolecular reactions. Researchers at Bruker Daltonik
in Germany have also developed genoSNIP, a method for single-nucleotide polymorphism (SNP) genotyping by MALDI-TOF
mass spectrometry.3  This method uses size reduction of primer extension products by incorporation of the photocleavable
linker for phototriggering strand breaks near to the 3’ end of the extension primer.  PC Linker can be incorporated into
oligonucleotides at any position by standard automated DNA synthesis methodology.   PC Linker Phosphoramidite has
the added advantage in that photocleavage results in monophosphate fragments at both the 3’- and 5’-termini of theoligonucleotide fragments.

(Please inquire for availability of vials andcolumns for other instrument types.)

INTELLECTUAL PROPERTY

ItemCatalog No.

Pack

PC Linker phosphoramidite isavailable from Glen Research inassociation with Link Technologies
Ltd (Scotland).

PC Biotin Phosphoramidite

10-4950-95
10-4950-90
10-4950-02

50 µmole
100 µmole
0.25g

PC Biotin NHS Ester

50-4950-22

4.2 mgPC Amino-Modifier Phosphoramidite

10-4906-90
10-4906-02

100 µmole
0.25g

PC Spacer Phosphoramidite

10-4913-90
10-4913-02

100 µmole
0.25g

PC Linker Phosphoramidite

10-4920-90
10-4920-02

100 µmole
0.25g

RELATED
5’-Biotin....................................105O

REFERENCES(1) P. Ordoukhanian and J-S. Taylor, J.
Am. Chem. Soc., 117, 9570-9571,
1995.
(2a) F. Hausch and A. Jäschke, Nucleic
Acids Research, 2000, 28, e35.
(2b) F. Hausch and A. Jäschke,
Tetrahedron, 2001, 57, 1261-1268.
(3) T. Wenzel, T. Elssner, K. Fahr, J.
Bimmler, S. Richter, I. Thomas,
and M. Kostrzewa, Nucleosides,
Nucleotides & Nucleic Acids, 2003,
22, 1579-1581.

DMTN

H3C

NH

S

O

NH

NH

O

NO 2

O CNEtPC Biotin

H3C

TFAHN

O
NH

PC Amino-Modifier92

O P N(iPr)2

PC Biotin NHS Ester

H3C

O P N(iPr)2
NO 2

O CNEtDMTOOO P N(iPr)2
NO 2

NH

PC Spacer

O CNEtDMTO

O P N(iPr)2
O CNEtNO 2

PC Linker

MODIFIERSCONJUGATION USING CLICK CHEMISTRY

Oligonucleotides bearing a single nucleosidic alkyne group can be prepared using  a C8-Alkyne-dC or dT-CE Phosphoramidite.  
Purified oligonucleotides are usually modified with 2-5 equivalents of the corresponding marker-azide (e.g., fluorescentdye azides). After the addition of precomplexed Cu(I), complete conversion to the labeled oligo is observed in a time span
between 30 min and 4 hours. After a simple precipitation step, labeled oligonucleotides can be recovered in near quantitative
yields. Using a combination of C8-Alkyne, C8-TIPS-Alkyne and C8-TMS-Alkyne, it is possible to label oligonucleotides in up to
three separate click reactions. The alkyne groups on the last two monomers are protected, respectively, with triisopropylsilyl(TIPS) and trimethylsilyl (TMS) protecting groups.5,6  The first click reaction on solid phase on a C8-Alkyne yields the singly
modified oligonucleotide with full retention of the TIPS and/or TMS protecting group.  For double click, a C8-TIPS-Alkyne isused as the second nucleoside and the TIPS protecting group is cleaved with tetrabutylammonium fluoride (TBAF) withoutcausing any damage to the DNA.  The second click reaction in solution yields the doubly modified oligonucleotide in excellent
yield. For the introduction of three different labels, all three nucleosides are introduced into oligonucleotides. The firstclick reaction is performed directly on the resin. The singly modified oligonucleotide is subsequently cleaved from the
support with concomitant cleavage of the TMS group and retention of the TIPS protecting group. The second click reaction
is performed in solution. Precipitation of the doubly modified oligonucleotide, cleavage of the TIPS group with TBAF, anda subsequent third click reaction in solution furnishes the desired triply modified oligonucleotide in excellent overall yield.
Item

Catalog No.

Pack

C8-Alkyne-dT-CE Phosphoramidite

10-1540-95
10-1540-90
10-1540-02

50 µmole
100 µmole
0.25g

C8-TIPS-Alkyne-dC-CE Phosphoramidite

10-1541

Discontinued

C8-TMS-Alkyne-dC-CE Phosphoramidite

10-1542

Discontinued

C8-Alkyne-dC-CE Phosphoramidite

10-1543-95
10-1543-90
10-1543-02

50 µmole
100 µmole
0.25g

TIPS
NHBz

O
HN

DMTO

N
N

O

DMTO

O

O

P

N(iPr)2O

CNEt

C8-Alkyne-dT

P

N(iPr)2O

CNEt

C8-TIPS-Alkyne-dC

N

N

O
DMTO

O

O

NHBz

N
N

O

TMS

NHBz

O

P

N(iPr)2O

CNEt

C8-TMS-Alkyne-dC[1] C.W. Tornoe, C. Christensen, M.
Meldal, J. Org. Chem. 2002, 67,3057-3064; V. V. Rostovtsev, L. G.
Green, V. V. Fokin, K. B. Sharpless,Angew. Chem. 2002, 114, 27082711; Angew. Chem. Int. Ed. 2002,
41, 2596-2599.
[2] C. J. Burrows, J. G. Muller, Chem.
Rev. 1998, 98, 1109 – 1151.
[3] T. R. Chan, R. Hilgraf, K. B.
Sharpless, V. V. Fokin, Org. Lett.
2004, 6, 2853 – 2855.
[4] J. Gierlich, G. A. Burley, P. M. E.
Gramlich, D. M. Hammond, T.
Carell, Org. Lett. 2006, 8, 36393642. F. Seela, V. R. Sirivolu, Chem.
Biodiversity 2006, 3, 509-514.
[5] P. M. E. Gramlich, S. Warncke, J.
Gierlich, T. Carell, Angew. Chem.
2008, 120, 3491–3493; Angew.
Chem. Int. Ed. 2008, 47, 3442–
3444.
[6] P. M. E. Gramlich, C. T. Wirges, A.
Manetto, T. Carell, Angew. Chem.
Int. Ed. 2008, 47, 8350-8358.

INTELLECTUAL PROPERTY
baseclick GmbH has been granted
the following patents (1-3) besides its
further patent applications (4-5).
1. WO  2006/117161  (New  labeling  strategies  for  the  sensitive detection of analytes)
2. WO 2008/952775 (Click chemistry
for the production of reportermolecules)
3. WO 2010/115957 (Click Chemistryon heterogeneous catalysts)
4. PCT/EP 2013/064610(Anandamide-modified nucleic
molecules)
5. PCT/EP 2015/056007 (Selfassembly of DNA Origami: adiagnostic tool)
baseclick GmbH holds a worldwide
exclusive license for granted patentapplication WO 03/101972 (Coppercatalysed ligation of azides andacetylenes  for  the  nucleic  acid field)in the area of diagnostics and research.
As Glen Research and baseclick arepartners, Glen Research is now able tohelp in sublicensing this outstanding
technology.

N

O
DMTO

O

REFERENCES

O

O

P

N(iPr)2O

CNEt

C8-Alkyne-dC

93

MODIFICATION/LABELINGThe copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction between azides and alkynes to form 1,2,3-triazoles,
as reported1 by Sharpless, was found to be so exquisitely regioselective and efficient at even the most mild conditions
that Sharpless coined the term ‘Click Chemistry’ to describe it.  The use of this method for DNA modification has beensomewhat delayed by the fact that copper ions damage DNA, typically yielding strand breaks.2  As these problems havenow been overcome by the use of copper(I)-stabilizing ligands (e.g., tris(benzyltriazolylmethyl)amine, TBTA3), Carell et al.
and Seela et al. discovered that the CuAAC reaction can be used to functionalize alkyne-modified DNA nucleobases withextremely high efficiency.4

MODIFIERSCONJUGATION USING CLICK CHEMISTRY (CONT.)
RELATED

5-Ethynyl-dU offers convenient click conjugation with an azide to generate a label rigidly attached to one of the oligonucleotide
bases.  5-Ethynyl-dU is subject to base-catalyzed hydration during cleavage and deprotection, especially when using a strong
base or heat.  Hydration of an ethynyl group forms a methyl ketone which subsequently blocks potential click reactions.  
Mild deprotection conditions are necessary when using 5-Ethynyl-dU-CE Phosphoramidite to prevent this side reaction.  
TIPS-5-Ethynyl-dU-CE Phosphoramidite, containing a protected alkyne, offers broader compatibility with oligonucleotide
synthesis and deprotection.  Protecting the 5-ethynyl group with a triisopropylsilyl (TIPS) protecting group prevents acidor base catalyzed hydration during oligonucleotide synthesis and workup.  A quick treatment with TBAF removes the TIPS
protecting group.

3’-Propargyl-5-Me-dC CPG........70

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Item

Catalog No.

Add

C8-TIPS-Alkyne-dT-CE Phosphoramidite

10-1544

Discontinued

Expedite
MerMadeE
M

C8-TMS-Alkyne-dT-CE Phosphoramidite

10-1545

Discontinued

Columns
For Instrument type

5-Ethynyl-dU-CE Phosphoramidite
Add

Expedite
Applied Biosystems 3900
MerMadeEA
M

10-1554-95
10-1554-90
10-1554-02

50 µmole
100 µmole
0.25g

TIPS-5-Ethynyl-dU-CE Phosphoramidite

10-1555-95
10-1555-90
10-1555-02

50 µmole
100 µmole
0.25g

THPTA Ligand(Water soluble)

50-1004-92
50-1004-90

25 µmole
100 µmole

Click-Solution (DMSO/t-BuOH)

50-1002-11

10 x 1.0mL

Monomers
For Instrument type

(Please inquire for availability of vials andcolumns for other instrument types.)

TIPS
O

P

N(iPr)2O

CNEt

C8-TIPS-Alkyne-dT

94

DMTO

O

O

O

P

N(iPr)2O

CNEt

C8-TMS-Alkyne-dT

HN

N

O

N

O
DMTO

O

O

O
HN

HN
N

O
DMTO

TMS

O

HN

Pack

O

P

N(iPr)2O

CNEt

5-Ethynyl-dU

N

O
DMTO

O

O

O

P

N(iPr)2O

CNEt

TIPS-5-Ethynyl-dU

TIPS

MODIFIERSCONJUGATION USING CLICK CHEMISTRY (CONT.)

Item

Catalog No.

Pack

5’-Hexynyl Phosphoramidite

10-1908-90
10-1908-02

100 µmole
0.25g

Azidobutyrate NHS Ester(Dissolve 2.3mg in 60µL of DMSO)

50-1904-23
50-1904-24

2.3mg
23mg

5’-Bromohexyl Phosphoramidite

10-1946-90
10-1946-02

100 µmole
0.25g

Alkyne-NHS Ester(Dissolve 2.3mg in 60µL of DMSO)

50-1905-23
50-1905-24

2.3mg
23mg

Alkyne-Modifier Serinol Phosphoramidite

10-1992-95
10-1992-90
10-1992-02

50 µmole
100 µmole
0.25g

3’-Alkyne-Modifier Serinol CPG

20-2992-01
20-2992-10
20-2992-42
20-2992-41
20-2992-13
20-2992-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

REFERENCES(1) R. Kumar, et al., Journal of theAmerican Chemical Society, 2007,
129, 6859-6864.
(2) J. Lietard, A. Meyer, J.J. Vasseur,and F. Morvan, Tetrahedron Letters,
2007, 48, 8795-8798.

RELATED
Serinol Products.......................100

MODIFICATION/LABELING

Oligonucleotides prepared using 5’-Hexynyl Phosphoramidite are stable to standard deprotection conditions andexhibit a slightly increased retention time on RP HPLC.  Azides are not compatible with oligonucleotide synthesis using
phosphoramidites so a post-synthesis reaction is required. Azidobutyrate NHS Ester is used1 for azido-modification of aminesat either the 3’-end or the 5’-end of an oligo and it can even be used for internal modification on an Amino-Modifier-C6
dX residue within the sequence.  Specific to the 5’-terminus, 5’-Bromohexyl Phosphoramidite is added in the last cycle.
This modifier can then be easily transformed into a 5’-azido group by displacement of bromide using sodium azide.2
Alkyne NHS ester allows the functionalization of an amino moiety in a variety of molecules, including DNA and RNA
oligonucleotides as well as peptides or proteins. We also offer two products for use in Click Chemistry based upon our
1,3-diol product portfolio with the serinol backbone - a phosphoramidite for adding an alkyne group at the 5’ terminus
or within the sequence, and a synthesis support for labeling the 3’ terminus of oligonucleotides with an alkyne group.   

O
OP

N(iPr)2

O

CNEt

N3
O

5’-Hexynyl Phosphoramidite

O
O

O

O

O
O

Alkyne-NHS Ester

O

Azidobutyrate NHS Ester

O
N

Br

N

P

N(iPr)2O

CNEt

5’-Bromohexyl Phosphoramidite

ODMT

O
N
H

O

N
H

O

O
P

N(iPr)2O

CNEt

Alkyne-Modifier Serinol Phosphoramidite

O

ODMT

O
N
H

N
H

O

succinoyl CPG

3’-Alkyne-Modifier Serinol CPG

95

MODIFIERSCONJUGATION USING CLICK CHEMISTRY (CONT.)
RELATEDdSpacer.......................................90

STABILITY NOTES
Oligonucleotides containing a 5’-iodogroup are prepared conventionallywith the exception that deprotection
is carried out in ammoniumhydroxide at room temperature for24 hours.  Under these conditions,degradation of the iodo group wasless than 2%.

1-Ethynyl-dSpacer CE Phosphoramidite can be used in any position within an oligonucleotide while still retaining the highefficiency of click chemistry.  The modifier is efficiently incorporated into oligonucleotides using standard phosphoramidite
chemistry, is stable to common deprotection conditions, and is compatible with Glen-Pak™  purification.  1-Ethynyl-dSpacer
generates a substituted 1,2,3-triazole pseudo-nucleobase after click chemistry conjugation with an azide.  The 1-ethynyldSpacer modification exhibits similar duplex stability to the standard dSpacer (10-1914) and destabilizes the duplex wheninternally incorporated.  Upon cycloaddition, the duplex stability is moderated by the resulting structure of the modification.  
Simple 1,2,3-triazoles were destabilizing, as were modifications that incorporated TEG linkers (6-FAM-TEG and Amino-TEG).  
Modifications that incorporated aromatic functional groups restored duplex stability to varying degrees with coumarin andpsoralen significantly restoring stability.  A 5’-iodo-modified oligonucleotide (prepared using 5’-Iodo-dT) can be quantitatively
converted to the corresponding 5’-azide.

Item

Catalog No.

Pack

1-Ethynyl-dSpacer CE Phosphoramidite

10-1910-95
10-1910-90
10-1910-02

50 µmole
100 µmole
0.25g

5’-I-dT-CE Phosphoramidite

10-1931-90
10-1931-02

100 µmole
0.25g

OLIGO-CLICK KITS
Oligo-Click Kits has been discontinued. Please contact technical support.
Item

Catalog No.

baseclick Oligo-Click-M-Reload
baseclick Oligo-Click-M-Biotinbaseclick Oligo-Click-M-Fluoresceinbaseclick Oligo-Click-M-TAMRA

50-2100
50-210150-210250-2103

Pack
Discontinued
Discontinued
Discontinued
Discontinued

O
CH 3

HN
I

DMTO

O
O

P

N(iPr)2O

CNEt

1-Ethynyl-dSpacer

96

O

N
O

O P N(iPr)2
O CNEt5’-I-dT

MODIFIERS
COPPER-FREE CLICK CHEMISTRYAt Glen Research, our goal was to offer a copper-free click phosphoramidite reagent with the following properties:

OTHER INSTRUMENT TYPES

From the variety of cyclooctyne-based copper-free click reagents so far described, we have chosen to offer compounds basedon a dibenzo-cyclooctyne (DBCO) structure.  We are offering 5’-DBCO-TEG Phosphoramidite for preparing oligos with a 5’DBCO modification and DBCO-dT-CE Phosphoramidite for inserting a DBCO group at any position within the oligonucleotide.
In addition, we offer a further DBCO phosphoramidite – DBCO-Serinol Phosphoramidite.  Using our proprietary serinol
backbone as a non-nucleosidic spacer allows the DBCO group to be placed at any location within a sequence with multiple
additions clearly possible. DBCO-sulfo-NHS Ester is also offered for post-synthesis conjugation reactions.  DBCO-modified
oligos may be conjugated with azides in organic solvents, such as DMSO, or aqueous buffers. Depending on the azide used,
the reaction will go to completion in 4-17 hours at room temperature.  Simple desalting on a Glen Gel-Pak™ leads to a
product with virtually quantitative conjugation efficiency.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M

Note: We now recommend that synthesis of oligos containing DBCO-dT be completed using 0.5 M CSO in anhydrous
acetonitrile (40-4632-xx).  Acceptable results can be achieved with iodine oxidation if DBCO-dT is subjected to no morethan 8-10 cycles.  

(Please inquire for availability of vials andcolumns for other instrument types.)

RELATED
Item

Catalog No.

Pack

5’-DBCO-TEG Phosphoramidite    

10-1941-95
10-1941-90
10-1941-02

50 µmole
100 µmole
0.25g

DBCO-dT-CE Phosphoramidite    

10-1539-95
10-1539-90
10-1539-02

50 µmole
100 µmole
0.25g

DBCO-sulfo-NHS Ester(Dissolve 5.2mg in 60µL water or DMSO)

50-1941-23
50-1941-24

5.2mg
52mg

DBCO-Serinol Phosphoramidite  10-1998-95
10-1998-90
10-1998-02

50 µmole
100 µmole
0.25g

N

H
N

O

O

O

O

O

O

P

N(iPr)2

O

CNEt

O

N
O

H
N
O

DBCO-Serinol

DBCO-dTO

OP

N(iPr)2

O

CNEt

O

OCNEt
O
ODMT

P

NiPr2

O

O

N

O
DMTO

N

H
N

N
H

HN

5’-DBCO-TEG

O

0.5M CSO....................................36
Serinol Products.......................100

N
O

O

SO3Na

N

O

DBCO-sulfo-NHS Ester

O

97

MODIFICATION/LABELINGAll minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

• Simple to use• Stable in solution on the synthesizer• Stable to ammonium hydroxide and AMA• Excellent click performance in 17 hours or less at room temperature

MODIFIERSCONJUGATION USING CLICK CHEMISTRY (CONT.)REFERENCE

Glen Research is offering first our most popular labels for general interest and, subsequently, we will add azide productsthat are not compatible with phosphoramidite chemistry.  

(1) J. Gierlich, G.A. Burley, P.M. Gramlich,
D.M. Hammond, and T. Carell, Org Lett,
2006, 8, 3639-42.

Biotin is still our most commonly used label and biotinTEG, with its hydrophilic triethylene glycol spacer, is the most popularbiotin product.  Desthiobiotin is a biotin analogue that is well captured by streptavidin but the captured product can be easily
released by applying a biotin solution to the streptavidin beads.  6-FAM is our most popular fluorescein derivative and we offer
azides of both 6-FAM and pivaloyl-protected 6-FAM for situations where subsequent reactions require the 6-FAM to be protected.  
In both 6-FAM products, the hydrophilic TEG spacer is again used.  The azides are offered in 25 and 100 µmole packs for convenientoligonucleotide labeling.
7-Hydroxycoumarin, also known as umbelliferone, is a highly fluorescent, pH-sensitive fluorophore that emits in the blue
region of the spectrum.  However, its fluorescence is strongly quenched if the hydroxyl is alkylated or phosphorylated, making
it useful in high-throughput screening for phosphatases and lipases.  Interestingly, it was found that the 3-azido derivativeis also highly quenched but, upon reaction with an alkyne in the presence of copper to form the triazole, the fluorescenceis restored.1  The clicked coumarin emits at a lambda max of 480 nm and absorbs at 358 nm.
HEX and TET are two of our most popular fluorescein-based dyes for labeling oligonucleotides.  We are happy to offer 6-HEX
and 6-TET Azides for use in click conjugations.
Item

Catalog No.

Pack

BiotinTEG Azide

50-2000-92
50-2000-90

25 µmole
100 µmole

DesthiobiotinTEG Azide

50-2001-92
50-2001-90

25 µmole
100 µmole

Dipivaloyl 6-FAM-TEG Azide

50-2002-92
50-2002-90

25 µmole
100 µmole

6-FAM-TEG Azide

50-2003-92
50-2003-90

25 µmole
100 µmole

Coumarin Azide

50-2004-92
50-2004-90

25 µmole
100 µmole

6-HEX Azide

50-2005-92
50-2005-90

25 µmole
100 µmole

6-TET Azide

50-2006-92
50-2006-90

25 µmole
100 µmole

O
HN

O
HN

NH
H
N

S

O

O

NH

O

O

O

HO

O

O

Cl

OH

HO

O

O

O

O

N3
N3

Cl

O

Dipivaloyl 6-FAM-TEG Azide

O

N3

HN

O

O
O

Cl

Cl

O
O

Coumarin Azide

O

O

O

98

O

DesthiobiotinTEG Azide

O
O

HN

O

O

O

BiotinTEG Azide
O

HO

H
N

N3

O

O

6-FAM-TEG Azide

O

N3

HO

Cl

Cl

O

N3

6-HEX Azide

OH
Cl

O
Cl

O
Cl

HN

OH

O

O
Cl

HN

6-TET Azide

N3

MODIFIERSCONJUGATION USING CLICK CHEMISTRY (CONT.)
Two nitroxide spin labels, TEMPO Azide and TEMPO-TEG Azide, for site directed spin labeling (SDSL) are now offered.
Click Chemistry with psoralen azide and one of our many nucleosidic and non-nucleosidic alkyne derivatives has thepotential to generate a variety of practical cross-linkers.  The well known reversible cross-linking behavior of psoralen withan adjacent thymidine residue could be very useful.

Item

Catalog No.

Pack

TEMPO Azide

50-2007-92
50-2007-90

25 µmole
100 µmole

TEMPO-TEG Azide

50-2008

Discontinued

Psoralen Azide

50-2009-92
50-2009-90

25 µmole
100 µmole

Disulfo-Cyanine 7 Azide

50-2010

Discontinued

SO3-K+

-O S
3

N

N+

N3

O

MODIFICATION/LABELING

To better address applications in near-infrared (NIR) imaging, Glen Research is offering a water soluble Disulfo-Cyanine 7
azide that can be easily conjugated to DNA and RNA through standard click chemistry.  This long wavelength dye offers thebenefits of improved solubility, reduced aggregation, and improved stability in the near-infrared spectrum along with theconvenience of click chemistry.

O
O
•O

N

N3

•O

N

O

N3

O

O

O

N3

H
N
O

TEMPO Azide

TEMPO-TEG Azide

Psoralen Azide

Disulfo-Cyanine 7 Azide

99

LABELINGSERINOL REAGENTS FOR MODIFICATION AND LABELINGOTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

INTELLECTUAL PROPERTY
Serinol Reagents for Modification andLabeling are covered by US Patent No.:8,394,948.

Most popular non-nucleosidic phosphoramidites for modification and labeling are based on two structural types:  1,2-diols
and 1,3-diols.  Products based on a 1,2-diol backbone were first described to allow amino-modification and biotin labeling.  
Technically, the 1,2-diol backbone has some drawbacks relative to the 1,3-diol backbone.   The 1,2-diol backbone canparticipate in a dephosphorylation reaction since the 1,2-diol can form a favored 5-membered cyclic phosphate intermediate.  
This reaction is competitive with simple hydrolysis of the protecting groups and leads to some loss of label.  However, thedegree of loss at the 3’ terminus can be limited by the removal of the cyanoethyl protecting group using DBU or diethylamineprior to the cleavage and deprotection steps.  Similarly, loss at the 5’ terminus can be eliminated by retaining the DMT groupuntil the oligo is fully deprotected.  Fortunately, the elimination reaction is virtually non-existent in the 1,3-diol backbone
since the cyclic intermediate would be a 6-membered ring which is not favored for a cyclic phosphate intermediate.
IVD customers have requested a new backbone based on a 1,3-diol that would overcome any technical or IP issues surrounding
our current products.  We now offer a line of products based on the serinol backbone, which have been developed in close
collaboration between Glen Research and Nelson Biotechnologies.  Protected Biotin Serinol Phosphoramidite and CPG areprotected with a t-butylbenzoyl group on the biotin ring.  This group is designed to stop any phosphoramidite reactions at
this active position in biotin.  This protection avoids branching when using nucleophilic activators like DCI.  The protecting
group is easily removed during oligonucleotide cleavage and deprotection.  The BiotinLC versions are similarly protected
and should be useful for the synthesis of highly sensitive biotinylated probes.  6-Fluorescein Serinol Phosphoramidite and
CPG are designed to prepare oligonucleotides containing one or several 6-Fluorescein (6-FAM) residues.  Amino-Modifier
Serinol Phosphoramidite and CPG are used to add amino groups into one or several positions in oligonucleotides.  The aminogroup is protected with Fmoc, which may be removed on the synthesis column prior to solid-phase conjugation to the aminogroups, or which may be removed during deprotection for subsequent solution phase conjugation to the amino groups.
Combining lipoic acid and our patented serinol backbone, we now offer Dithiol Serinol Phosphoramidite and the related  3’-Dithiol Serinol CPG.  This unique architecture moves the bulky dithiol away from the phosphate backbone, making it suitablefor conjugation to gold surfaces.  The long spacer arm of Dithiol Serinol also allows multiple consecutive incorporations of themodifier without the need for intermediate spacer phosphoramidite additions to achieve optimal stepwise coupling efficiency.
We offer three products for use in Click Chemistry based upon our 1,3-diol product portfolio with the serinol backbone - a
phosphoramidite for adding an alkyne group at the 5’ terminus or within the sequence, a synthesis support for labeling the
3’ terminus of oligonucleotides with an alkyne group, and DBCO-Serinol phosphoramidite as a copper-free click reagent.

Item

Catalog No.

Pack

Protected Biotin Serinol Phosphoramidite

10-1993-95
10-1993-90
10-1993-02

50 µmole
100 µmole
0.25g

6-Fluorescein Serinol Phosphoramidite

10-1994-95
10-1994-90
10-1994-02

50 µmole
100 µmole
0.25g

O

O

O

N

O
NH

O
H
N

S
O

H
N
O

Protected Biotin Serinol Phosphoramidite

100

O

O

O

O

O

ODMT
O

P

N(iPr)2

O

CNEt

H
N

HN
O

ODMT
O

P

N(iPr)2O

CNEt

6-Fluorescein Serinol Phosphoramidite

LABELINGSERINOL REAGENTS FOR MODIFICATION AND LABELING (CONT.)
Item

Catalog No.

Pack

Protected BiotinLC Serinol Phosphoramidite

10-1995-95
10-1995-90
10-1995-02

50 µmole
100 µmole
0.25g

Amino-Modifier Serinol Phosphoramidite

10-1997-95
10-1997-90
10-1997-02

50 µmole
100 µmole
0.25g

Dithiol Serinol Phosphoramidite

10-1991-95
10-1991-90
10-1991-02

50 µmole
100 µmole
0.25g

Alkyne-Modifier Serinol Phosphoramidite

10-1992-95
10-1992-90
10-1992-02

50 µmole
100 µmole
0.25g

DBCO-Serinol Phosphoramidite  10-1998-95
10-1998-90
10-1998-02

50 µmole
100 µmole
0.25g

RELATED

O

O
N

NH
H
N

S

O

O

H
N

O

H
N

O

ODMT

O

O

O

O

Protected BiotinLC Serinol Phosphoramidite

Fmoc

H
N

H
N

ODMT

O

O

S

P

N(iPr)2

O

CNEt

O

N
H

N
H

O

O

P

N(iPr)2

O

CNEt

ODMT
O

P

N(iPr)2

O-CNEtDithiol Serinol

ODMT

O

H
N

H
N
S

Amino-Modifier Serinol Phosphoramidite

O

MODIFICATION/LABELING

DBCO...........................................97

N
P

N(iPr)2O

CNEt

Alkyne-Modifier Serinol Phosphoramidite

O

H
N
O

OCNEt
O

P

NiPr2

ODMT

DBCO-Serinol

101

LABELINGSERINOL REAGENTS FOR MODIFICATION AND LABELING (CONT.)OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

Item

Catalog No.

Pack

3’-Protected Biotin Serinol CPG

20-2993-01
20-2993-10
20-2993-42
20-2993-41
20-2993-13
20-2993-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2994-01
20-2994-10
20-2994-42
20-2994-41
20-2994-13
20-2994-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2997-01
20-2997-10
20-2997-42
20-2997-41
20-2997-13
20-2997-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2999-01
20-2999-10
20-2999-42
20-2999-41
20-2999-13
20-2999-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
3’-6-Fluorescein Serinol CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3’-Amino-Modifier Serinol CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
3’-Azido-Modifier Serinol CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

O

O

O
N

O

O

NH
H
N

H
N

S

O

O

3'-Protected Biotin Serinol CPG

O
O

O
O

ODMT
O-succinyl-CPG

O
H
N

HN
O

ODMT
O-succinyl-CPG

3'--6-Fluorescein Serinol CPG

Fmoc

H
N

H
N
O

ODMT
O-succinyl-CPG

3'-Amino-Modifier Serinol CPG

102

3'-Azido-Modifier Serinol CPG

LABELINGSERINOL REAGENTS FOR MODIFICATION AND LABELING (CONT.)
Item

Catalog No.

Pack

3’-Dithiol Serinol CPG

20-2991-01
20-2991-10
20-2991-42
20-2991-41
20-2991-13
20-2991-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2992-01
20-2992-10
20-2992-42
20-2992-41
20-2992-13
20-2992-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
3’-Alkyne-Modifier Serinol CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

INTELLECTUAL PROPERTYThis product is covered under US
Patent 8,945,515 B2.

COT SERINOL PHOSPHORAMIDITE

S

Item

Catalog No.

COT Serinol Phosphoramidite

10-1996

H
N

H
N
S

O

O

3’-Dithiol Serinol CPG

O

ODMT
O

succinoyl-CPG

O

N
H

Pack
Discontinued

N
H

O

H
N

H
N

ODMT

O

MODIFICATION/LABELINGCOT Serinol Phosphoramidites has been discontinued.  Please contact technical support.

succinoyl CPG

3’-Alkyne-Modifier Serinol CPG

O

O

ODMT
O

P

N(iPr)2

O-CNEtCOT Serinol

103

LABELINGDABCYL LABELINGREFERENCE

A molecular beacon probe1 has its natural fluorescence quenched in solution unless it is hybridized to the target sequence.  
Consequently, the design of a molecular beacon requires a fluorophore to be in one part of the sequence and the quencher
molecule to be in another, with both molecules being separated from the oligonucleotide by a hydrocarbon spacer.  
The Dabcyl group has been found to be a universal quencher.  3’-Dabsyl CPG and 3’-Dabcyl CPG are used to prepare probeswith the quencher blocking the 3’-terminus.   5’-Dabcyl Phosphoramidite locates the quencher at the 5’-terminus andDabcyl-dT places it within the sequence, leaving the 3’-terminus available for polymerase extension.

(1) S. Tyagi and F.R. Kramer, Nature
Biotechnology, 1996, 4, 303-308.

Cy5

Cy5.5

Cy3.5

Cy3

TMR

TET

____ Eclipse

HEX____ Dabcyl

FAM

DYE QUENCHER PLOT____ BHQ-1

Item

Catalog No.

Pack

3’-Dabsyl CPG

20-5911-01
20-5911-10
20-5911-41
20-5911-42
20-5911-13
20-5911-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-5912-01
20-5912-10
20-5912-41
20-5912-42
20-5912-13
20-5912-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

26-5912-01
26-5912-10
26-5912-52
26-5912-55

0.1g
1.0g
Pack of 10
Pack of 10

Dabcyl-dT    

10-1058-95
10-1058-90
10-1058-02

50 µmole
100 µmole
0.25g

5’-Dabcyl Phosphoramidite    10-5912-95
10-5912-90
10-5912-02

50 µmole
100 µmole
0.25g____ BHQ-2____ BHQ-3____ BBQ-650

300

400

500

600

700

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

800

wavelength (nm)https://www.glenresearch.com/spectralcharacteristics-of-fluorescent-dyes

3’-Dabcyl CPG
1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
3'-Dabcyl PS
200 nmole columns (ABI 3900)
40 nmole columns (ABI 3900)

O
O

DMTO

NH CPG
O

O

HN

O

SO 2

N

DMTO
N

NH CPG

O

O

O

DMTO

O

O

N

HN

N(Me) 2NO

Dabsyl CPG

HNO

N(Me) 2

Dabcyl CPG

O
NH

NH

N
O

N

N(Me) 2(Me) 2NO P N(iPr)2

N

H
N

N
O

O CNEt104

N

Dabcyl-dT

5’-Dabcyl Phosphoramidite

O P N(iPr)2
O CNEtLABELING
BIOTIN LABELING

Item

Catalog No.

Pack

Biotin Phosphoramidite

10-1953-95
10-1953-90
10-1953-02

50 µmole
100 µmole
0.25g

BiotinTEG Phosphoramidite

10-1955-95
10-1955-90
10-1955-02

50 µmole
100 µmole
0.25g

Protected Biotin Serinol Phosphoramidite

10-1993-95
10-1993-90
10-1993-02

50 µmole
100 µmole
0.25g

Protected BiotinLC Serinol Phosphoramidite

10-1995-95
10-1995-90
10-1995-02

50 µmole
100 µmole
0.25g

O
NH

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

MODIFICATION/LABELING

Glen Research biotin phosphoramidites for direct labeling of synthetic oligonucleotides exhibit the following features:
1. All are soluble in acetonitrile at concentrations useful for DNA synthesis.
2. All include a DMT group for cartridge purifications which is essential for the preparation of biotinylated PCR primers
because of the potential for cross contamination in HPLC purifications.
3. For the development of diagnostic probes, biotin phosphoramidite is capable of branching to allow multiple biotins to
be introduced at the 3’- or 5’-terminus.  BiotinTEG Phosphoramidite contains a 15 atom mixed polarity spacer arm basedon a triethylene glycol.  
4. Protected Biotin Serinol Phosphoramidite and CPG are protected with a t-butylbenzoyl group on the biotin ring.  
This group is designed to stop any phosphoramidite reactions at this active position in biotin.  This protection avoids
branching when using nucleophilic activators like DCI.  The protecting group is easily removed during oligonucleotide
cleavage and deprotection.  The BiotinLC versions are similarly protected and should be useful for the synthesis of highly
sensitive biotinylated probes.

O
NH

NH
NH

S

ODMT

O

NH
NH

S

O

O

O

O

O P N(iPr)2

O CNEtOON

BiotinTEG Phosphoramidite
NH
H
N

S

N

H
N

O

O

O

O

Protected Biotin Serinol Phosphoramidite

ODMT
O

NH
H
N

S

O

ODMT
O P N(iPr)2

O CNEtBiotin Phosphoramidite

O

O

O

O

Protected BiotinLC Serinol Phosphoramidite

H
N

H
N

O
O

O

P

N(iPr)2

O

CNEt

ODMT
O

P

N(iPr)2

O

CNEt

105

LABELING
BIOTIN LABELING (CONT.)
RELATED

Biotin-dT can replace dT residues within the oligonucleotide sequence.  5’-Biotin phosphoramidite can be added ONLY ONCE
to the 5’-terminus of an oligonucleotide.  However, the DMT group on the biotin can be used in RP cartridge and HPLC
purification techniques.  PC Biotin is a photocleavable 5’-biotin phosphoramidite.  BiotinTEG CPG and Protected BiotinLC
Serinol CPG are  designed for the direct synthesis of oligonucleotides containing biotin at the 3’ terminus.  

PC Biotin.....................................92

Desthiobiotin is a biotin analogue that exhibits lower binding to biotin-binding proteins such as streptavidin.  This biotin
analogue is lacking the sulfur group from the molecule and has a dissociation constant (Kd) several orders of magnitudeless than biotin/streptavidin.  As a result, biomolecules containing desthiobiotin are dissociated from streptavidin simply
in the presence of buffered solutions of biotin.  We offer desthiobiotinTEG phosphoramidite and the corresponding CPG.
ABI-style vials and columns are supplied unless otherwise requested (see note box).

IItem

Catalog No.

Pack

5’-Biotin Phosphoramidite

10-5950-95
10-5950-90
10-5950-02

50 µmole
100 µmole
0.25g

5’-Biotin II Phosphoramidite

10-1954-95
10-1954-90
10-1954-02

50 µmole
100 µmole
0.25g

Biotin-dT

10-1038-95
10-1038-90
10-1038-02

50 µmole
100 µmole
0.25g

PC Biotin Phosphoramidite

10-4950-95
10-4950-90
10-4950-02

50 µmole
100 µmole
0.25g

DesthiobiotinTEG Phosphoramidite

10-1952-95
10-1952-90
10-1952-02

50 µmole
100 µmole
0.25g

O

O
HN
O

DMTO

HN

O
NH

NH

O

N

O

O

N
S

NH

NH
NH

O
O P N(iPr)2
O CNEtOOOO CNEtBiotin-dT
O
DMTN

NH
NH

S

O

5’-Biotin Phosphoramidite

106

ODMT
O P N(iPr)2

DesthiobiotinTEG Phosphoramidite

O
DMTN

O

O

O P N(iPr)2S

O CNEt5’-Biotin Phosphoramidite

H3C

NH
NH
O

O
NH

PC Biotin Phosphoramidite

O P N(iPr)2
NO 2

O CNEtLABELING
BIOTIN LABELING (CONT.)
Catalog No.

Pack

3’-BiotinTEG CPG

20-2955-01
20-2955-10
20-2955-42
20-2955-41
20-2955-13
20-2955-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
3’-BiotinTEG PS
200 nmole columns (ABI 3900)
40 nmole columns (ABI 3900)
3’-Protected Biotin Serinol CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3’-Protected BiotinLC Serinol CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
DesthiobiotinTEG CPG
0.2 µmole columns
1 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)26-2955-01
26-2955-10
26-2955-52
26-2955-55

0.1g
1.0g
Pack of 10
Pack of 10

20-2993-01
20-2993-10
20-2993-42
20-2993-41
20-2993-13
20-2993-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2995-01
20-2995-10
20-2995-42
20-2995-41
20-2995-13
20-2995-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2952-01
20-2952-10
20-2952-42
20-2952-41
20-2952-13
20-2952-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

MODIFICATION/LABELING

Item

O

O
N

NH

O

O

O

H
N

H
N

S

NH

ODMT
O-succinyl-CPG

Protected Biotin Serinol CPG

NH
NH

S

O

O

O
N

O

O

O

O

ODMT
O -succinyl-lcaa-CPG

BiotinTEG CPG

NH
H
N

S

O

O

H
N

O

O

Protected BiotinLC Serinol CPG

O
NH

H
N

O
O

O

ODMT
O-succinyl-CPG

NH
NH
O

O

O

DesthiobiotinTEG CPG

O

O

ODMT
O-succinyl-lcaa-CPG

107

LABELINGFLUORESCEIN LABELING

Cy55’-Fluorescein phosphoramidite contains no 4,4’-dimethoxytrityl (DMT) group and can be added only once at the 5’-terminus,
thereby terminating synthesis.   This product is prepared using the 6-carboxyfluorescein derivative.   The tetrachloro-,
hexachloro-and dichloro-dimethoxy-fluorescein (TET, HEX and JOE, respectively) phosphoramidites are designed totake advantage of the multicolor detection capability of modern DNA sequencers and genetic analyzers.   Fluorescein
phosphoramidite is designed to produce the same fluorescein-type structure as had been previously prepared using
fluorescein isothiocyanate (FITC).  Our fluorescein phosphoramidite also contains a DMT group to allow quantificationof coupling.   The analogous structure, 6-Fluorescein Phosphoramidite, prepared using 6-FAM, is also available, alongwith 6-Fluorescein Serinol Phosphoramidite.  Fluorescein-dT and JOE-dT can be inserted into the desired sequence as areplacement for a dT residue.

Cy5.5

Cy3.5

Cy3

TMR

____ Eclipse

TET

FAM

____ Dabcyl

HEX

DYE QUENCHER PLOT____ BHQ-1____ BHQ-2____ BHQ-3____ BBQ-650

300

400

500

600

700

800

wavelength (nm)https://www.glenresearch.com/spectralcharacteristics-of-fluorescent-dyes

We offer five fluorescein supports.  Fluorescein CPG has traditionally been used to add the fluorescein label at the 3’-terminus.  
The analogous structure, 3’-(6-Fluorescein) CPG, prepared using 6-FAM, is now also available, along with 6-Fluorescein
Serinol CPG.  We also offer 3’-(6-FAM) CPG and Fluorescein-dT CPG, both derivatives of 6-carboxyfluorescein (6-FAM).  
Both  are single isomers and use an amide linkage which is stable during cleavage and deprotection and does not allow isomerformation.  3’-(6-FAM) CPG allows effective blockage of the 3’-terminus from polymerase extension as well as exonuclease
digestion.  Fluorescein-dT CPG allows both of these enzymatic activities to proceed.  Normal cleavage and deprotection
with ammonium hydroxide readily generates the fluorescein labeled oligos.
The NHS ester provides the option for post-deprotection labeling. When paired with a 5’-amino-modifier C6 (10-1906, 101907, 10-1916 or 10-1947), the resulting product would be identical to that generated with 5’-Fluorescein Phosphoramidite(10-5901).
The spectral characteristics of these dyes are detailed on the following page.

OO

10-5901-95
10-5901-90
10-5901-02

50 µmole
100 µmole
0.25g

5’-Hexachloro-Fluorescein
Phosphoramidite(HEX)

10-5902-95
10-5902-90
10-5902-02

50 µmole
100 µmole
0.25g

5’-Tetrachloro-Fluorescein
Phosphoramidite(TET)

10-5903-95
10-5903-90
10-5903-02

50 µmole
100 µmole
0.25g

Cl

O

O

Cl

Cl
O

Cl

CN

O
N

5’-Fluorescein Phosphoramidite

HN

O

O
Cl

O

O

O

O P

108

5’-Fluorescein Phosphoramidite(6-FAM)O
O

HN

Cat. No.

O

O
O

Item

O

O

Cl

CN

O
O P

N

5’-Hexachloro-Fluorescein
Phosphoramidite

HN

Cl

O
Cl

O

O

O
Cl

Cl

O

Pack

O

O

O

O
O

MeO

OMe

O
O

O
Cl

Cl

O

CN

O
O P

HN

N

5’-Tetrachloro-Fluorescein
Phosphoramidite

CN

O

O
O

P

N

5’-Dichloro-dimethoxy-Fluorescein
Phosphoramidite II

LABELINGFLUORESCEIN LABELING (CONT.)
Cat. No.

5’-Dichloro-dimethoxy-Fluorescein Phosphoramidite II(JOE)

10-5906-95
10-5906-90
10-5906-02

50 µmole
100 µmole
0.25g

JOE-dT Phosphoramidite    10-5936-95
10-5936-90
10-5936-02

50 µmole
100 µmole
0.25g

Fluorescein Phosphoramidite

10-1963-95
10-1963-90
10-1963-02

50 µmole
100 µmole
0.25g

FLUORESCENT DYES

Pack

Absorbance Emission
Maximum Maximum

Color

Fluorescein

494nm

525nm

Green

Tetrachloro-

521nm

536nm

Orange

535nm

556nm

Pink

SIMA (HEX)

538nm

551nm

Pink

Dichloro-

525nm

548nm

Orange/
Pink

TAMRA

565nm

580nm

Rose

Cy3

546nm

563nm

Red

Cy3.5

588nm

604nm

Purple

Cy5

646nm

662nm

Violet

Cy5.5

683nm

707nm

Dark Blue

Yakima Yellow

530nm

549nm

Yellow

Redmond Red

579nm

595nm

Red

Fluorescein
HexachloroFluorescein

dimethoxy-

6-Fluorescein Phosphoramidite

10-1964-95
10-1964-90
10-1964-02

6-Fluorescein Serinol Phosphoramidite

50 µmole
100 µmole
0.25g

Fluorescein-dT Phosphoramidite    

10-1056-95
10-1056-90
10-1056-02

50 µmole
100 µmole
0.25g

Fluorescein NHS ester  50-5901-22
50-5901-25

2.4mg
9.5mg

O

DMTO

O
NH

NH

HN

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

O

O

O

OTHER INSTRUMENT TYPES

O

O

O

50 µmole
100 µmole
0.25g

10-1994-95
10-1994-90
10-1994-02

O

Fluorescein

O
O

N

O

O P N(iPr)2

Fluorescein dT

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

JOE-dT

O CNEt
O

O

O

O

O

O
O
O

O

O

O

O

O

O
O

O

O

O

O

O

O

O
O

NH
ODMT
O P

N(iPr)2

O CNEt6-Fluorescein Phosphoramidite

HN
H
N

HN
O

ODMT
O

P

N(iPr)2O

CNEt

6-Fluorescein Serinol Phosphoramidite

NH
S

ODMT
O P

Fluorescein NHS ester

N(iPr)2

O CNEtFluorescein Phosphoramidite

109

MODIFICATION/LABELING

Item

LABELINGFLUORESCEIN LABELING (CONT.)

Cy5

Cy5.5

Cy3.5

Cy3

TMR

____ Eclipse

TET

FAM

____ Dabcyl

HEX

DYE QUENCHER PLOT____ BHQ-1

Item

Cat. No.

3’-Fluorescein CPG

20-2963-01
20-2963-10
20-2963-41
20-2963-42
20-2963-13
20-2963-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2964-01
20-2964-10
20-2964-41
20-2964-42
20-2964-13
20-2964-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-2961-01
20-2961-10
20-2961-41
20-2961-42
20-2961-13
20-2961-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

26-2961-01
26-2961-10
26-2961-52
26-2961-55

0.1g
1.0g
Pack of 10
Pack of 10

20-2994

Discontinued

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)____ BHQ-2____ BHQ-3____ BBQ-650

3’-(6-Fluorescein) CPG
300

400

500

600

700

800

wavelength (nm)1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)https://www.glenresearch.com/spectralcharacteristics-of-fluorescent-dyes3’-(6-FAM) CPG
1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)3’-(6-FAM) PS
200 nmole columns (ABI 3900)
40 nmole columns (ABI 3900)
3’-6-Fluorescein Serinol CPG

O

O

O

O

O

O
O

NH
S

110

O

O

O-succinyl-CPG

O

O
O

O

ODMT
O-succinyl-CPG

3’-6-Fluorescein Serinol CPG

O

O

O

O

O

O
NH
ODMT

O

O

O

O
NH

H
N

HN

O

O
O

O

ODMT

3’-Fluorescein CPG

O

O

O

O
HN

O

O

Pack

O

O
ODMT

O -succinyl-CPG

3’-(6-Fluorescein) CPG

NHO

3’-(6-FAM) CPG

CPG

LABELINGFLUORESCEIN LABELING (CONT.)FLUORESCEIN LABELING (SIMA)
Dichloro-diphenyl-fluorescein,  SIMA (HEX) exhibits virtually identical absorbance and emission spectra to HEX.  SIMA (HEX)
is much more stable to basic deprotection conditions than HEX and oligonucleotides can be deprotected using ammoniumhydroxide at elevated temperatures and even ammonium hydroxide/methylamine (AMA) at room temperature or 65°C for
10 minutes.  SIMA absorption maximum was 3 nm blue-shifted compared to HEX at pH 7.  The absorbance is broader, so
the extinction coefficient is smaller than that of HEX, but when exciting at 500 nm where the absorbance was normalized,
the emission was still 90% of HEX and the emission was red-shifted by 5 nm.  A second SIMA (HEX) product, SIMA (HEX)-dT,
can be used to introduce SIMA (HEX) in the synthetic oligonucleotide sequence, usually as a replacement for the nativedT linkage.  Again, this product is fully compatible with deprotection schemes using ammonium hydroxide at elevatedtemperatures or AMA at room temperature and 65°C.

SIMA (HEX)-dT Phosphoramidite

O

O

DMTO

O

O

50 µmole
100 µmole
0.25g

O
NH

NH

Expedite
Applied Biosystems 3900
MerMadeE
A
M____ Dabcyl____ Eclipse____ BHQ-1____ BHQ-2____ BHQ-3____ BBQ-650

300

400

500

O

N

O -Succinyl-lcaa-CPG
O

3’-Fluorescein-dT CPG

O

O

O
O
O

O

O

O

HN

N
H

HN

O
Cl

O

CN

Cl

O
O

P

SIMA (HEX) Phosphoramidite

O

O

O

O

N

600

700

wavelength (nm)

O

O

Cy5

DYE QUENCHER PLOT

https://www.glenresearch.com/spectralcharacteristics-of-fluorescent-dyes

O

O

HN

10-5945-95
10-5945-90
10-5945-02
OOO

50 µmole
100 µmole
0.25g

Add

(Please inquire for availability of vials andcolumns for other instrument types.)Pack

10-5905-95
10-5905-90
10-5905-02

Columns
For Instrument type

O
Cl

O

N

O
DMTO

Cl
H
N

O

O

P

N(iPr)2O

CNEt

SIMA (HEX)-dT Phosphoramidite

111

MODIFICATION/LABELINGSIMA (HEX) Phosphoramidite

E
M

Cy5.5

Cat. No.

Add

Expedite
MerMade

Cy3.5

Item

Monomers
For Instrument typeCy3

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

TMR

20-2056-01
20-2056-10
20-2056-41
20-2056-42
20-2056-13
20-2056-14

TET

3’-Fluorescein-dT CPG

OTHER INSTRUMENT TYPES

Pack

HEX

Cat. No.

FAM

Item

800

LABELINGCYANINE LABELING
SPECTRAL DATA FORCYANINE DYES
Absorbance Emission
Maximum Maximum

Two cyanine derivatives, Cyanine 3 and Cyanine 5, which differ in structure simply by the number of carbons in the
conjugated polyene linkage, are joined by the closely related analogues, Cyanine 3.5 and Cyanine 5.5, and are available asphosphoramidites.  Cyanine dyes are normally added once at the 5’-terminus and the MMT group should be removed on
the synthesizer.  The absorbance of the MMT cation (yellow) is noticeably different from the DMT cation (orange), and so,
absorbance-based trityl monitors will detect it incorrectly as a low coupling.  On the other hand, conductivity detectors
will interpret the release more correctly.  Cyanine dye phosphoramidites have also been used successfully adjacent to
the 3’-terminus. Cyanine 3 and Cyanine 5 supports are also offered to allow simpler production of 3’ cyanine dye-labeledoligonucleotides.

Color

Cyanine 3

546nm

563nm

Red

Cyanine 3.5

588nm

604nm

PurpleCyanine 5

646nm

662nm

VioletCyanine 5.5

683nm

707nm

Dark Blue

Cyanine 7

750nm

773nm

Dark Green

Deprotection of oligos containing Cyanine dyes may be carried out with ammonium hydroxide at room temperature,
regardless of the base protecting groups on the monomers used.  If there is a need to use ammonium hydroxide at elevatedtemperature, Cyanine 3 and Cyanine 3.5 are more stable than Cyanine 5 and Cyanine 5.5.  However, it is always prudent touse monomers with base labile protecting groups to limit the exposure time to 2 hours or less at 65°C during deprotection.

(Measured in an oligo in 0.1M TEAA buffer, pH7.)

Cy5

To better address applications in near-infrared (NIR) imaging, Glen Research is offering a water soluble Disulfo-Cyanine 7
azide that can be easily conjugated to DNA and RNA through standard click chemistry.  This long wavelength dye offers thebenefits of improved solubility, reduced aggregation, and improved stability in the near-infrared spectrum along with theconvenience of click chemistry.

Cy5.5

Cy3

TMR

Cy3.5

____ Eclipse

TET

FAM

____ Dabcyl

HEX

DYE QUENCHER PLOT____ BHQ-1____ BHQ-2____ BHQ-3____ BBQ-650

This NHS ester versions allows for post-deprotection labeling, and unlike the phosphoramidite versions, contains 2 sulfonate
substitutions directly on the indocyanine nuclei. The sulfonates make the Cyanine 3 and 5 less susceptible to aggregationand do not significantly change the fluorescent properties of the dyes.
300

400

500

600

700

wavelength (nm)https://www.glenresearch.com/spectralcharacteristics-of-fluorescent-dyes

NO

Cat. No.

Cyanine 3 Phosphoramidite

10-5913-95
10-5913-90
10-5913-02

50 µmole
100 µmole
0.25g

Cyanine 3.5 Phosphoramidite

10-5914-95
10-5914-90
10-5914-02

50 µmole
100 µmole
0.25g

Cyanine 5 Phosphoramidite

10-5915-95
10-5915-90
10-5915-02

50 µmole
100 µmole
0.25g

Cyanine 5.5 Phosphoramidite

10-5916-95
10-5916-90
10-5916-02

50 µmole
100 µmole
0.25g

N

N

Cl

P

N(iPr)2O

CNEt

Cyanine 3 Phosphoramidite

112

Item

N

N

Cl
OMMT

800

OMMT

N

N

Cl

O

P

N(iPr)2O

CNEt

Cyanine 3.5 Phosphoramidite

Pack

N

IOMMT

O

P

N(iPr)2O

CNEt

Cyanine 5 Phosphoramidite

OMMT

O

P

N(iPr)2O

CNEt

Cyanine 5.5 Phosphoramidite

LABELINGCYANINE LABELING (CONT.)

20-5913-01
20-5913-10
20-5913-41
20-5913-42

0.1g
1.0g
Pack of 4
Pack of 4

20-5915-01
20-5915-10
20-5915-41
20-5915-42

0.1g
1.0g
Pack of 4
Pack of 4

Disulfo-Cyanine 7 Azide

50-2010-92
50-2010-90

25 µmole
100 µmole

sulfoCyanine 3 NHS Ester

50-5913-22

3.8mg

Cyanine 3 CPG
1 µmole columns (TWIST format only)
0.2 µmole columns
Cyanine 5 CPG
1 µmole columns (TWIST format only)
0.2 µmole columns

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

DYE QUENCHER PLOT
FAM____ Dabcyl____ Eclipse____ BHQ-1____ BHQ-2

sulfoCyanine 5 NHS Ester

50-5915-22____ BHQ-3

3.9mg____ BBQ-650

300

400

500

600

700

wavelength (nm)https://www.glenresearch.com/spectralcharacteristics-of-fluorescent-dyes
Quasar® 570-dT Phosphoramidite

Quasar® 670-dT Phosphoramidite
N

N

Cl
OMMT

N
N

N+

sulfoCyanine 3 NHS EsterN

Cyanine 5 CPG

Cl
OMMT

N3

O

O

H
N
O

Disulfo-Cyanine 7 Azide

O

O

SO3-K+-O S
3sulfoCyanine 5 NHS EsterOO

Cyanine 3 CPG

N
H

113

N
H

MODIFICATION/LABELING

50 µmole
100 µmole
0.25g

Cy5

10-5955-95
10-5955-90
10-5955-02

Cy5.5

Quasar® 670-dT Phosphoramidite

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Cy3.5

50 µmole
100 µmole
0.25g

Cy3

10-5953-95
10-5953-90
10-5953-02

TMR

Quasar® 570-dT Phosphoramidite

OTHER INSTRUMENT TYPES

Pack

TET

Cat. No.

HEX

Item

800

LABELING
ELITECHGROUP DYES AND QUENCHER
FLUORESCENT DYES
Absorbance Emission
Maximum Maximum

Glen Research’s agreement with ELITechGroup, formerly Epoch Biosciences, allows us to offer several of their proprietaryproducts designed for the synthesis of novel DNA probes.  We are pleased to offer products based on ELITechGroup’s RedmondRed®, Yakima Yellow® and AquaPhluor® 593 fluorophores and Eclipse® non-fluorescent quencher.  Under our agreement wealso supply PPG, a modified nucleoside, and 5’-Aldehyde-Modifier C2 Phosphoramidite.  The fluorescent dyes, Yakima Yellow,
Redmond Red and AquaPhluor 593, are available as phosphoramidites and supports.  Yakima Yellow has an absorbancemaximum at 530 nm and emission maximum at 549 nm, Redmond Red’s absorbance and emission maxima are at 579 nm
and 595 nm, respectively, and AquaPhluor 593 has an absorbance maximum at 593 nm and emission maximum at 613 nm.   

Color

YakimaYellow

530nm

549nm

Yellow

Redmond
Red

579nm

595nm

Red

AquaPhluor
593

593nm

613nm

Red

The Eclipse quencher from ELITechGroup solves most of the problems inherent in the synthesis of molecular beacon and
FRET probes.  The Eclipse molecule is highly stable and can be used safely in all common oligo deprotection schemes.  
The absorbance maximum for Eclipse Quencher is at 522 nm, compared to 479 nm for dabcyl.  In addition, the structureof the Eclipse Quencher is substantially more electron deficient than that of dabcyl and this leads to better quenching overa wider range of dyes, especially those with emission maxima at longer wavelengths (red shifted) such as Redmond Red
and Cyanine 5.  In addition, with an absorption range from 390 nm to 625 nm, the Eclipse Quencher is capable of effective
performance in a wide range of colored FRET probes.

INTELLECTUAL PROPERTY
These Products are for research
purposes only, and may not be used
for commercial, clinical, diagnostic
or any other use. These Products
are subject to proprietary rights of
ELITechGroup and are made and soldunder license from ELITechGroup.
There is no implied license forcommercial use with respect tothese Products and a license must be
obtained directly from ELITechGroup
with respect to any proposedcommercial use of these Products.
“Commercial use” includes but is not
limited to the sale, lease, license orother transfer of the Product or any
material derived or produced from it,
the sale, lease, license or other grantof rights to use the Product or any
material derived or produced from it,or the use of the Product to perform
services for a fee for third parties(including contract research).

ItemCat. No.

Pack

Redmond Red® Phosphoramidite

10-5920-95
10-5920-90
10-5920-02

50 µmole
100 µmole
0.25g

Yakima Yellow® Phosphoramidite

10-5921-95
10-5921-90
10-5921-02

50 µmole
100 µmole
0.25g

5’-AquaPhluor® 593 Phosphoramidite

A simple agreement must be signed
before end-users and custom oligo
services may purchase theseproducts for use as defined above.  
https://www.glenresearch.
com/media/productattach/
import/technical_note/
ELITechGroupProducts.pdf

10-5923-95
10-5923-90
10-5923-02

50 µmole
100 µmole
0.25g

5’-AquaPhluor® 639 Phosphoramidite

10-5926-95
10-5926-90
10-5926-02

50 µmole
100 µmole
0.25g

AquaPhluor®, Yakima Yellow®,
Redmond Red® and Eclipse®,are registered Trademarks of
ELITechGroup.

Eclipse® Quencher Phosphoramidite

10-5925-95
10-5925-90
10-5925-02

50 µmole
100 µmole
0.25g

O 2N

O

Cl

O

N
N

O P N

Epoch Eclipse™ Quencher
O 2N

N
CH 3

O

CH 2CH 2CN

O

Eclipse® Quencher CPG

114

N
CH 3

N
O

Cl

NH CPG
O

O
Cl
Cl

O DMT

O

O
NH

O

O

O

N
N

O

O

O P N

O

O

CH 3

CH 2CH 2CN

O

O

O

Cl
O

O

O

C 49H60Cl 4ON3O 10P O DMT
1023.81
YakimaYellow® CPG
1021.277044
Cl C 57.5% H 5.9% Cl 13.9% N 4.1% O 15.6% P 3.0%

O

O

O P N

O

O
N

N

Redmond Red®

O DMT
O

O
O

CH 2CH 2CN

O

NH CPGN
Yakima Yellow Phosphoramidite

O

O

O

Yakima Yellow®

Cl

O DMT

Cl

Cl

Cl

O
N

CH 3

O
N

Redmond Red® CPG

Redmond Red CPG

O

O
N
O

O DMT

NH CPGOLABELING
ELITECHGROUP DYES AND QUENCHER (CONT.)

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

DYE QUENCHER PLOT____ Dabcyl____ Eclipse____ BHQ-1

AquaPhluor® 639 CPG

20-5926-01
20-5926-10
20-5926-41
20-5926-42
20-5926-13
20-5926-14

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)____ BHQ-2

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1____ BHQ-3____ BBQ-650

300

400

500

600

700

wavelength (nm)

Eclipse® Quencher CPG

20-5925-01
20-5925-10
20-5925-41
20-5925-42
20-5925-13
20-5925-14

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

PF6-

N+

O

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

N

https://www.glenresearch.com/spectralcharacteristics-of-fluorescent-dyes

RELATED
PPG..............................................63
5’-Aldehyde-Modifier C2...........89

N

CPG

N

O

HN
O

O

N

N

N+

O

O

P

5’-AquaPhluor® 593

O

O

O

NH
F 3C

P

O

N
DMTO

O

O

N
O

N

O

-O

P

N

O

H
N

NH-CPG

AquaPhluor® 593 CPG

O

O

P

N

O
O

O

Cl

O

F3C
O

O

N
O

N

O

N

O

O
O

5’-AquaPhluor® 639

O

Cl

DMTO

N

P

O
O

AquaPhluor® 639 CPG

SO3-

O

P

N(iPr)2

O

CNEt

115

SO3
H
N

CF3
O

MODIFICATION/LABELING

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)20-5923-01
20-5923-10
20-5923-41
20-5923-42
20-5923-13
20-5923-14

E
M

Cy5

AquaPhluor® 593 CPG

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

Cy5.5

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)20-5921-01
20-5921-10
20-5921-41
20-5921-42
20-5921-13
20-5921-14

Add

Expedite
MerMadeCy3

Yakima Yellow® CPG

Monomers
For Instrument typeTMR

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

Cy3.5

20-5920-01
20-5920-10
20-5920-41
20-5920-42
20-5920-13
20-5920-14

TET

Redmond Red® CPG

OTHER INSTRUMENT TYPES

Pack

HEX

Cat. No.

FAM

Item

800

LABELING
BLACK HOLE QUENCHER DYESTABLE 1: BLACK HOLEQUENCHERS
Quencher lmax
(nm)
BHQ-1
BHQ-2
BHQ-3

534
579
672

E260
(L/mol.cm)

Emax(L/mol.cm)

8,000
8,000
13,00034,00038,00042,700With the growing popularity of red and near-infrared dyes, we are offering the Black Hole QuencherTM dyes (BHQs), whose
physical properties are detailed in Table 1.  BHQ dyes are robust dark quenchers that very nicely complement our existingproduct line.  They are compatible with ammonium hydroxide deprotection, exhibit excellent coupling efficiencies, havelarge extinction coefficients and are completely non-fluorescent.  Their absorbances are well-tuned to quench a varietyof popular fluorophores – even those far into the red, such as Cy3 and Cy5.  The dark quencher most typically used in a
Molecular Beacon is Dabcyl.  Because the quenching does not involve FRET, there is little, if any, dependence upon donoracceptor spectral overlap.  In a comprehensive paper by Marras, Kramer and Tyagi,1 the ability of BHQ-1 and BHQ-2 toquench 22 different fluorophores was evaluated.  For shorter wavelength fluorophores such as fluorescein, the quenchingefficiency was roughly the same as Dabcyl (91% – 93%).  However, for dyes emitting in the far red, such as Cy5, the BHQdyes were far superior – quenching the Cy5 with 96% efficiency, compared to 84% with Dabcyl.  This may reflect the BHQ’s
ability to form stable, non-fluorescent complexes which can be a plus even in FRET probes.  Indeed, recent work suggeststhat these non-fluorescent complexes will form even in the absence of a hairpin stem structure used by Molecular Beacons.2

REFERENCES(1) S.A.E. Marras, F.R. Kramer, and S.
Tyagi, Nucleic Acids Res., 2002, 30,E122.
(2) M.K. Johansson, H. Fidder, D. Dick,and R.M. Cook, J Am Chem Soc,
2002, 124, 6950-6956.

RELATED
Dabcyl.......................................104
Eclipse™....................................114
BBQ-650®.................................118

INTELLECTUAL PROPERTY"Black Hole Quencher", "BHQ-0","BHQ-1", "BHQ-2" and "BHQ-3"
are trademarks of BiosearchTechnologies, Inc., Novato, CA.  
The BHQ dye technology is the
subject of pending patents and islicensed and sold under agreementwith Biosearch Technologies, Inc..  
Products incorporating the BHQ dye
moiety are sold exclusively for R&D
use by the end-user.  They may not
be used for clinical or diagnostic
purposes and they may not be resold, distributed or re-packaged.

ItemCat. No.

5’-BHQ-1 Phosphoramidite    10-5931-95
10-5931-90
10-5931-02

50 µmole
100 µmole
0.25g

5’-BHQ-2 Phosphoramidite    10-5932-95
10-5932-90
10-5932-02

50 µmole
100 µmole
0.25g

BHQ-1-dT    

10-5941-95
10-5941-90
10-5941-02

50 µmole
100 µmole
0.25g

BHQ-2-dT    

10-5942-95
10-5942-90
10-5942-02

50 µmole
100 µmole
0.25g

H3C

N
NO 2

H3C
N

N

N

O 2N

N
O P N(iPr)2

OCH 3

Pack

H3CO
N
N

HN
DMTO

O

O

N

O P N(iPr)2
O CNEt

116

N

O
NH

O

NH
O

N

CH 3O

N

N

CH 3
O

O 2N

HN
DMTO

BHQ-1-dTN
O P N(iPr)2
O CNEt5’-BHQ-2

CH 3
N

N

OCH 3

O CNEt5’-BHQ-1

O

N

O

O

N

O P N(iPr)2
O CNEt

N

O
NH

O

NH
O

BHQ-2-dT

N

N

CH 3O

OCH 3
N
N

NO 2

LABELING
BLACK HOLE QUENCHER DYES (CONT.)

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

DYE QUENCHER PLOT____ Dabcyl____ Eclipse____ BHQ-1____ BHQ-2____ BHQ-3____ BBQ-650

300

400

500

600

700

wavelength (nm)https://www.glenresearch.com/spectralcharacteristics-of-fluorescent-dyes

H3C

N
NO 2

ODMT

H3C
N

N

N

N

O-glycolate-CPG

OCH 33'-BHQ-1 CPG

O 2N

H3CO
N
N

ODMT
N

N

OCH 3

3'-BHQ-2 CPG

O-glycolate-CPG

ODMT

N

N
N

N

+

-

X

N

N

N
O-glycolate-CPG

3'-BHQ-3 CPG

117

MODIFICATION/LABELING

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)20-5933-01
20-5933-10
20-5933-41
20-5933-42
20-5933-13
20-5933-14

E
M

Cy5

3'-BHQ-3 CPG

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

Cy5.5

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)20-5932-01
20-5932-10
20-5932-41
20-5932-42
20-5932-13
20-5932-14

Add

Expedite
MerMadeCy3.5

3'-BHQ-2 CPG

Monomers
For Instrument typeCy3

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

TMR

20-5931-01
20-5931-10
20-5931-41
20-5931-42
20-5931-13
20-5931-14

TET

3'-BHQ-1 CPG

OTHER INSTRUMENT TYPES

Pack

HEX

Cat. No.

FAM

Item

800

LABELING
BLACKBERRY® QUENCHER (BBQ-650®)
INTELLECTUAL PROPERTYBlackBerry® Quencher technology:
US Patent 7,879,986. The purchaseof BlackBerry® Quencher reagentsincludes a limited license to
use these reagents exclusively
for research and development
purposes. They may not be used forclinical or diagnostic purposes andthey may not be re-sold, distributed,
or re-packaged without prioragreement and consent of Berry& Associates, Inc. Subsequent saleof products that are derived fromBlackBerry® Quencher reagents ispermitted so long as the following
written disclaimer is included in
written and electronic catalogs, incommercial advertisement, and inpackages with containers of suchderivative products: “BlackBerry is
a trademark of Berry & Associates,
Inc. Products derived fromBlackBerry® Quencher reagents are
sold exclusively for research anddevelopment use by the purchaser.
They may not be used for clinical or
diagnostic purposes without prioragreement and consent of Berry &Associates, Inc.”We are happy to offer several products containing the BlackBerry® Quencher (BBQ-650®), which exhibits a broad absorption
profile from 550 nm to 750 nm, centered at 650 nm. This range offers more effective quenching of some of our popular
long wavelength dyes like TAMRA, Redmond Red, Cy dyes and DyLight dyes. We offer BBQ-650 products for the 3’ and 5’
termini, as well as BBQ-650-dT for inclusion within the oligonucleotide sequence, with the following properties:• Quenches the fluorescence of long wavelength dyes
• Quenches in FRET and contact mode
• Absorbance maximum at ~650 nm• Quenching range – 550-750 nm• Compatible with standard oligo synthesis chemistry• Compatible with regular deprotection but requires mild deprotection with AMA at room temperature• Available for 3’, 5’, and internal substitution• More stable than BHQ-3

ItemCat. No.

5’-BBQ-650® Phosphoramidite    10-5934-95
10-5934-90
10-5934-02

50 µmole
100 µmole
0.25g

BBQ-650®-dT    10-5944-95
10-5944-90
10-5944-02

50 µmole
100 µmole
0.25g

3’-BBQ-650® CPG

20-5934-01
20-5934-10
20-5934-41
20-5934-42
20-5934-13
20-5934-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)PackN
glycolate-lcaa-CPG

-

O
N

O

O
N

N

H3CO

P

N(iPr)2

O

CNEt

H3CO

OCH3
N

N

N

N

N

N

N

OCH3

O2N

NO2

5’-BBQ-650™

3’-BBQ™-650™ CPG
O

H
N
O
H3CO

N

O
DMTO

O
N
H

HN

N

O

O

118

O

DMTO

P

N(iPr)2

O

CNEt

O2N

BBQ-650™-dT

N

O
N

N

OCH3

O

N

N

O 2C
O
NHS

+

LABELINGRHODAMINE (TAMRA) LABELING

ROX is a rhodamine dye that has played a significant role in dideoxy Sanger sequencing alongside FAM, JOE and TAMRA. The
dye itself is also commonly used for qPCR applications as a passive reference dye. ROX is not available as a phosphoramidite,and as such, the use of this NHS ester is the standard method of incorporating ROX into oligonucleotides. This NHS ester
is offered as the 6-isomer.

Item

Cat. No.

3’-TAMRA CPG

20-5910-01
20-5910-10
20-5910-41
20-5910-42

0.1g
1.0g
Pack of 4
Pack of 4

26-5910-01
26-5910-10
26-5910-52
26-5910-55

0.1g
1.0g
Pack of 10
Pack of 10

TAMRA-dT    

10-1057-95
10-1057-90
10-1057-02

50 µmole
100 µmole
0.25g

TAMRA NHS Ester(Solution in anhydrous DMSO)

50-5910-66

60 µL

ROX NHS Ester

50-5911-22

3.2mg

1 µmole columns
0.2 µmole columns
3'-TAMRA PS
200 nmole columns (ABI 3900)
40 nmole columns (ABI 3900)

O

DMTO

O

NH

O

O

CPG

-

CO 2

O

N

HN

HN
O

O

TAMRA CPG

N

N

O

O

O CNEt

N

-

O

CO 2
NH

UltraMILD monomers................27

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

N

NH
O

N

O P N(iPr)2

+

O

-

DMTO

Pack

RELATEDON+TAMRA-dT

+

O 2C
O
NHS
TAMRA NHS Ester

ROX NHS Ester

119

MODIFICATION/LABELING

Rhodamine derivatives are not sufficiently stable to survive conventional deprotection and these must be attached toamino-modified oligonucleotides using post-synthesis labeling techniques.  Because Tetramethyl Rhodamine (TAMRA) is
not base stable, the procedure to cleave and deprotect the labeled oligonucleotide must be carefully considered.  Using
the UltraMILD monomers and deprotection with potassium carbonate in methanol, TAMRA oligonucleotides can be fairly
conveniently isolated.  To streamline the preparation of TAMRA oligos, we offer 3’-TAMRA CPG for 3’ labeling and TAMRA-dT
for labeling within the sequence.  We also offer TAMRA NHS ester for labeling amino-modified oligonucleotides.

LABELINGOTHER INSTRUMENT TYPESACRIDINE LABELING
Acridine phosphoramidite is designed to produce an oligonucleotide containing acridine at any position in the molecule.  
Acridine CPG is used to label the 3’-terminus.  Acridine is an effective intercalating agent.

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

Item

Cat. No.

Acridine Phosphoramidite

10-1973-95
10-1973-90
10-1973-02

50 µmole
100 µmole
0.25g

3’-Acridine CPG

20-2973-01
20-2973-10
20-2973-41
20-2973-42
20-2973-13
20-2973-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole cloumn (Expedite)Pack

DNP LABELINGAn analytical test based on detection of 2,4-dinitrophenyl (DNP) labeled oligonucleotides with anti-DNP antibodies has been
proposed.  We have chosen the branched triethylene glycol (TEG) spacer in our version of DNP phosphoramidite since it
can be added once or several times to the 3’ or 5’ terminus.

Item

Catalog No.

Pack

DNP-TEG Phosphoramidite

10-1985-95
10-1985-90
10-1985-02

50 µmole
100 µmole
0.25g

N

Cl
N

MeO
NH
ODMT

Cl

MeO
O 2N

NH
ODMT

O-P-N(iPr)2
O-CNEtAcridine120

O -succinyl-lcaa-CPG

Acridine CPG

NH

O

O

O

O

ODMT
O P N(iPr)2

NO 2

O CNEt

DNP-TEGLABELING
CHOLESTEROL LABELINGRELATED

Potential therapeutic oligonucleotides must permeate the cell membrane for optimal activity.  The addition of lipophilicgroups to an oligonucleotide would be expected to enhance cellular uptake/membrane permeation.  The use of cholesteryloligos and the consequent improvement in activity has been described.  We have designed our Cholesteryl products withtriethyleneglycol (TEG) spacers for maximum solubility.
Item

Catalog No.

Pack

Cholesteryl-TEG Phosphoramidite

10-1975-95
10-1975-90
10-1975-02

50 µmole
100 µmole
0.25g

5’-Cholesteryl-TEG Phosphoramidite

10-1976-95
10-1976-90
10-1976-02

50 µmole
100 µmole
0.25g

3’-Cholesteryl-TEG CPG

20-2975-01
20-2975-10
20-2975-41
20-2975-42
20-2975-13
20-2975-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

Spermine....................................54

MODIFICATION/LABELINGTOCOPHEROL LABELING
Vitamin E is both lipophilic and non-toxic even at high doses so would be an excellent candidate as a lipophilic carrier for
oligonucleotides.  Therefore, as an addition to our cholesteryl product line, we offer simple a-tocopheryl (vitamin E) labeling.  
Totally synthetic a-tocopherol is racemic at its three chiral centers and is used to prepare this product.
Item

Catalog No.

Pack

a-Tocopherol-TEG Phosphoramidite

10-1977-95
10-1977-90
10-1977-02

50 µmole
100 µmole
0.25g

STEARYL LABELING
We now offer a simple C18 lipid as an economical and effective carrier molecule.  We envisage that the 5’-stearyl groupwill become a favored lipophilic carrier for experimentation with synthetic oligonucleotides.
Item

Catalog No.

Pack

5’- Stearyl Phosphoramidite

10-1979-90
10-1979-02

100 µmole
0.25g

O
DMTO

O

CNEt

P

N(iPr)2
O

O

O
O

O

O

N
H

DMTO

P

N(iPr)2

H
N

O

O

O

O
O

O

N
H

O

5’-Cholesteryl-TEG

DMTO

N(iPr)2
O

O

O

O

O

a-Tocopherol-TEG

O
CNEt

CNEt

P

O

Cholesteryl-TEG

O

O

CPG
O

O
O

O

O

O

N
H

3’-Cholesteryl-TEG CPG

OO

5’- Stearyl

121

P

N(iPr)2O

CNEt

LABELING
N-ACETYLGALACTOSAMINE (GalNAc) LABELINGOTHER INSTRUMENT TYPES
A directed approach to the delivery of therapeutic oligonucleotides specifically to the liver has been to target theasialoglycoprotein receptor (ASGPR) using a suitable glycoconjugate.   Indeed, ASGPR is the ideal target for delivery oftherapeutic oligonucleotides to the liver since it combines tissue specificity, high expression levels and rapid internalizationand turnover.  The use of oligonucleotide glycoconjugates has led to significant advances in therapeutic delivery as evidenced
by the work of Alnylam Pharmaceuticals and Ionis Pharmaceuticals using multivalent N-acetylgalactosamine (GalNAc)
oligonucleotide conjugates.

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M

Glen Research is delighted to introduce a GalNAc modification strategy using a monomeric GalNAc support and theequivalent GalNAc phosphoramidite.  Our experimental work has shown that these products are fully compatible withregular oligonucleotide synthesis and deprotection.  Oligonucleotides containing GalNAc can be deprotected using standard
procedures during which the acetyl protecting groups on GalNAc are removed.  We have demonstrated that 5’-GalNAc C3
phosphoramidite can be used to prepare oligonucleotides with multiple consecutive GalNAc additions at the 5’ terminus.

(Please inquire for availability of vials andcolumns for other instrument types.)

Item

Catalog No.

Pack

5’-GalNAc C3 Phosphoramidite

10-1974-95
10-1974-90
10-1974-02

50 µmole
100 µmole
0.25g

GalNAc C3 CPG

20-2974-01
20-2974-10
20-2974-41
20-2974-42
20-2974-13
20-2974-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

INTELLECTUAL PROPERTY
Sold under the licensefrom AM Chemicals LLC
for Research Use Only,
including such researchin connection with
development of products tobe commercialized by EndUser.

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

PALMITATE LABELING
Palmitate Phosphoramidite is a saturated fatty acid with a 16-carbon backbone. This 5’-modification is a lipophilic group.
When incorporated into a synthetic oligonucleotide, Palmitate conjugates offer enhanced cellular uptake and delivery to
extrahepatic tissues.

OAc OAc
O

AcO
AcHN

Item

Catalog No.

Pack

Palmitate Phosphoramidite

10-1978-95
10-1978-90
10-1978-02

50 µmole
100 µmole
0.25g

O
O

OTMT
N
H

N
O

Palmitate Phosphoramidite
OAc OAc

O

O

O

AcO

GalNAc C3 CPG

122

AcHN
O

N
H

CPG

O
O

OTMT
N
H

5’-GalNAc C3 Phosphoramidite

N
O

O

P
O

N(iPr)2
CNEt

LABELING
CDPI3 MGB™ LABELING• Arrest of primer extension and PCR blockers• Short and fluorogenic PCR primers• Real-time PCR probes• miRNA Inhibitors
The simplest approach to MGB probe design is to use an MGB support, add a quencher molecule as the first addition andcomplete the synthesis with a 5’-fluorophore.  Alternatively, a fluorophore support could be used with the 5’ terminus
containing a quencher molecule followed by a final MGB addition at the 5’ terminus.  Glen Research offers 5’-CDPI3 MGB™
Phosphoramidite and 3’-CDPI3 MGB™ CPG.  
5’-CDPI3 MGB phosphoramidite was found to be hydrophobic enough that it required 10% THF in ACN to go completely
into solution at a 0.1 M concentration and required a 3 minute coupling time.  Deprotection can be carried out in EtOH/
NH4OH 1:3 (v/v) 17 hr at 55 °C and CDPI3 MGB is compatible with GlenPak™ purification.
With the CDPI3 MGB CPG, optimal results are obtained if UltraMild monomers and Cap A are used during synthesis alongwith 0.5 M CSO oxidizer.  However, the use of standard monomers with iodine oxidation followed by deprotection with
EtOH/NH4OH 1:3 (v/v) for 17 hr at 55 °C  will give acceptable results.

Item

Catalog No.

Pack

5’-CDPI3 MGB™ Phosphoramidite

10-5924-95
10-5924-90
10-5924-02

50 µmole
100 µmole
0.25g

CDPI3 MGB™ CPG

20-5924-01
20-5924-10
20-5924-41
20-5924-42
20-5924-13
20-5924-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)5’-CDPI3 MGB™ Phosphoramidite

LEGAL NOTICENOTICE TO PURCHASER:
LIMITED LICENSE
This product is sold under licensing
arrangements between ELITechGroup
Inc. and Glen Research.  The purchaseprice of this product includes limited,
nontransferable rights to use theproduct solely for activities of thepurchaser which are directly related
to human diagnostics.  Other uses,
including incorporation of the
product into another commercial
product, are prohibited without
additional license rights.  Forinformation on purchasing a license
to this product for purposes otherthan those stated above, contact:
ELITech Group Molecular Diagnostics,
21720 23rd Drive SE, Suite 150,
Bothell, WA 98021
Phone (425) 482-5555
Fax (425) 482-5550
Email: mdx@elitechgroup.com
This limited license permits the
person or legal entity to which thisproduct has been provided to use theproduct, and the data generated byuse of the product, only for humandiagnostics.  Neither ELITechGroup
Inc. nor its licensors grants any otherlicenses, expressed or implied for any
other purposes.
Some components of nucleic acidanalysis, such as specific methods
and compositions for manipulating orvisualizing nucleic acids for analysis,
may be covered by one or more
patents owned by other parties.  
Similarly, nucleic acids containing
specific nucleotide sequences may
be patented.  Making, using, offering
for sale, or selling such components
or nucleic acids may require one
or more licenses.  Nothing in thisdocument should be construed as
an authorization or implicit license
to make, use or sell any so covered
component or nucleic acid under any
such patents.

CDPI3 MGB™ CPG

123

MODIFICATION/LABELINGThe tripeptide of dihydropyrroloindole-carboxylate (CDPI3) is a minor groove binding (MGB) moiety derived from thenatural product CC-1065 with strong DNA binding properties. Synthetic oligonucleotides with covalently-attached CDPI3
have enhanced DNA affinity and have improved the hybridization properties of sequence-specific DNA probes. Short CDPI3oligonucleotides hybridize with single-stranded DNA to give more stable DNA duplexes than unmodified ODNs of similar
length.  CDPI3 MGB-oligonucleotide conjugates have been found to be useful in the following applications:

LABELINGMGB ECLIPSE® CPG
LEGAL NOTICENOTICE TO PURCHASER:
LIMITED LICENSE
This product is sold under licensing
arrangements between ELITechGroup
Inc. and Glen Research.  The purchaseprice of this product includes limited,
nontransferable rights to use theproduct solely for activities of thepurchaser which are directly related
to human diagnostics.  Other uses,
including incorporation of the
product into another commercial
product, are prohibited without
additional license rights.  Forinformation on purchasing a license
to this product for purposes otherthan those stated above, contact:
ELITech Group Molecular Diagnostics,
21720 23rd Drive SE, Suite 150,
Bothell, WA 98021
Phone (425) 482-5555
Fax (425) 482-5550
Email: mdx@elitechgroup.com
This limited license permits the
person or legal entity to which thisproduct has been provided to use theproduct, and the data generated byuse of the product, only for humandiagnostics.  Neither ELITechGroup
Inc. nor its licensors grants any otherlicenses, expressed or implied for any
other purposes.
Some components of nucleic acidanalysis, such as specific methods
and compositions for manipulating orvisualizing nucleic acids for analysis,
may be covered by one or more
patents owned by other parties.  
Similarly, nucleic acids containing
specific nucleotide sequences may
be patented.  Making, using, offering
for sale, or selling such components
or nucleic acids may require one
or more licenses.  Nothing in thisdocument should be construed as
an authorization or implicit license
to make, use or sell any so covered
component or nucleic acid under any
such patents.

MGB Eclipse® pairs a minor groove binding (MGB) tripeptide with a dark quencher. The MGB significantly enhances
hybridization while the Eclipse® has a broad absorption range that quenches many of the most common fluorophores
including FAM, HEX, TET and Yakima Yellow®. Together, MGB Eclipse® is an attractive group for the synthesis of hydrolysis
probes, the most common probe detection method for qPCR.

Item

Catalog No.

Pack

MGB Eclipse® CPG

20-5927-01
20-5927-10
20-5927-41
20-5927-42
20-5927-13
20-5927-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

PSORALEN LABELING
Psoralen C2 at the 5’-terminus of an oligonucleotide serves effectively as a cross-linking reagent in double-stranded
oligonucleotides.   The 6 atom spacer arm of Psoralen C6 allows cross-linking with a triplex oligonucleotide strand.  
Click Chemistry with psoralen azide and one of our many nucleosidic and non-nucleosidic alkyne derivatives has thepotential to generate a variety of practical cross-linkers.  The well known reversible cross-linking behavior of psoralen withan adjacent thymidine residue could be very useful.

ItemCat. No.

Pack

Psoralen C2 Phosphoramidite

10-1982-90
10-1982-02

100 µmole
0.25g

Psoralen C6 Phosphoramidite

10-1983-90
10-1983-02

100 µmole
0.25g

Psoralen Azide

50-2009-92
50-2009-90

25 µmole
100 µmole

CH 3

O

O

O

O
CH 3

O CNEtPsoralen C2

CH 3

O

O P N(iPr)2

CH 3

O

O

O

O P N(iPr)2
O CNEtCH 3

CH 3

Psoralen C6N3OMGB Eclipse® CPG

124

O

Psoralen Azide

OLABELINGEDTA LABELING

Item

Cat. No.

EDTA-C2-dT-CE Phosphoramidite

10-1059-95
10-1059-90
10-1059-02

OTHER INSTRUMENT TYPES

50 µmole
100 µmole
0.25g

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

With an excellent stability profile, ferrocene has always attracted considerable interest for DNA labeling to generate probes forelectrochemical detection.  Based on our Amino-Modifier C6-dT structure, Ferrocene-dT is easily added to oligonucleotides
with no disruption of regular hybridization behavior.  Multiple incorporations into an oligonucleotide probe are also simply
achieved.  Oligonucleotides are deprotected using standard techniques.  Ferrocene oligonucleotides should be stored under
Argon and aqueous solutions should be degassed immediately.
Cat. No.

Ferrocene-dT-CE Phosphoramidite

10-1576-95
10-1576-90
10-1576-02

O
O
HN
DMTO

O

O

EtO

O
NH

NH

N

N
O

N

OEt

HN

O
OEt

O

O P N(iPr)2

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

H
N

N
H

O

O

O

50 µmole
100 µmole
0.25g

O

N

O
DMTO

Pack

O

Methylene Blue II is covered underEuropean patent EP2820003 and US
patent US9540405 and is sold underlicense from the University of Lyon.

Pack

FERROCENE LABELINGItem

INTELLECTUAL PROPERTY

Fe

Ferrocene-dT

P

N(iPr)2O

CNEt

O CNEt

EDTA-C2-dT

125

MODIFICATION/LABELING

EDTA-C2-dT phosphoramidite contains the triethyl ester of EDTA which allows sequence-specific cleavage of single- anddouble-stranded DNA and RNA.  The cleavage reaction is only initiated once Fe(II) and dithiothreitol are added and so isreadily controlled.  Coupling of EDTA-dT is normal but cleavage and deprotection should be carried out with sodium hydroxide
in aqueous methanol (0.4M NaOH in methanol/water 4:1) overnight at room temperature.

LABELING
METHYLENE BLUE LABELING
Methylene Blue, which belongs to the phenothiazine family of dyes, is a unique dye with a variety of useful properties.  
Despite its high extinction coefficient in the visible region (81,000 L/mol•cm), it is weakly fluorescent due to its high rate ofintersystem crossing from the S1 excited state to the T1 triplet state.  This property makes it an excellent photosensitizer, andit has been used extensively to produce highly reactive singlet oxygen.  Methylene blue has the ability to both intercalate
in duplex DNA, preferring G:C over T:A base pairs, and can act as an electrochemical redox probe.  Methylene blue has also
been shown to be unmatched in performance as a redox-active reporter for electrochemical biosensors.
Earlier, we introduced Methylene Blue C3 Phosphoramidite but this product proved to have quite limited stability andhas been discontinued.  As an alternative option, we introduced Methylene Blue NHS Ester to allow researchers to label
amino-modified oligonucleotides with this interesting dye.  With the encouragement and technical expertise of Carole Chaix
and her colleagues at the University of Lyon, we decided to prepare an alternative structure that seemed to have a muchsuperior stability profile - Methylene Blue II Phosphoramidite.  Fortunately, this structure did indeed prove more stable andwe are now able to offer again a Methylene Blue Phosphoramidite.

Item

Cat. No.

Pack

Methylene Blue NHS Ester(Dissolve 5.4mg in 60µL of DMSO)

50-1960-23

5.4mg

Methylene Blue II Phosphoramidite

10-5961-95
10-5961-90
10-5961-02

50 µmole
100 µmole
0.25g

N
N

DMTO
N

S

O
Cl

N

P

N(iPr)2

O

CNEt

S+

N

N
O

ClO4O

O

N
O

Methylene Blue II

126

Methylene Blue NHS Ester

LABELINGLABELING WITH THIAZOLE ORANGEOTHER INSTRUMENT TYPES

Thiazole orange is an asymmetric cyanine dye whose fluorescence can be quite dependent on its local environment. When an
oligonucleotide labeled with thiazole orange is hybridized to its complementary sequence, the thiazole orange acts as an intercalator.
In addition to providing enhanced thermal stability, the dye adopts a mostly planar configuration resulting in significantly enhanced
fluorescence. This “light up” effect can be as high as 34-fold depending on the sequence and how the dye is attached. This NHS ester willallow simple functionalization of internally located amino modifications such as those generated with amino-modifier C6 dT (10-1039).
Item

Cat. No.

Pack

Thiazole Orange NHS Ester

50-1970-23

5.4mg

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeEA
M

FLUORESCENT DYES
Absorbance Emission
Maximum Maximum

Thiazole Orange NHS Ester

Excimer

Pyrene-dU

402nm

472nm

486nm

Perylene-dU

473nm

490nm

Not
Determined

127

MODIFICATION/LABELING(Please inquire for availability of vials andcolumns for other instrument types.)

LABELINGLABELING WITH POLYAROMATIC HYDROCARBONSREFERENCES(1) R.W. Roberts and J.W. Szostak, Proc.
Natl. Acad. Sci. USA, 1997, 94, 12297302.
(2) S. Sando and E.T. Kool, J Amer Chem
Soc, 2002, 124, 2096-2097.

Pyrene and perylene are fluorescent polycyclic aromatic hydrocarbons that have the ability to form ‘excited state dimers’
known as excimers.  This unstructured, long-wavelength emission arises from the formation of a charge-transfer complex
between the excited state and the ground state of two fluorescent molecules.  In Pyrene-dU and perylene-dU, the hydrocarbon
is attached at the 5 position of deoxyuridine through a triple bond and is electronically coupled to the deoxyuridine base.  
This electronic coupling of the base and the hydrocarbon makes the fluorescence sensitive to the base pairing of the dU
portion of the molecule, allowing the discrimination between perfect and one base mismatched targets.

RELATED
3’-Phosphate CPG......................88
Sulfurizing Reagent....................39
Fluorescein-dT..........................109

Item

Cat. No.

Pyrene-dU-CE Phosphoramidite

10-1590-95
10-1590-90
10-1590-02

50 µmole
100 µmole
0.25g

Perylene-dU-CE Phosphoramidite

10-1591-95
10-1591-90
10-1591-02

50 µmole
100 µmole
0.25g

PUROMYCIN CPG

Pack

One of the most challenging requirements associated with combinatorial chemistry is the recovery of sequence informationof the oligonucleotide or peptide selected by the screening assay.  A method1 has been developed to generate a fusion
product between mRNA and the polypeptide it encodes using in vitro translation of synthetic RNAs 3’-labeled with puromycin,
an antibiotic that mimics transfer RNA.  Puromycin binds in the ribosome’s A site, forms a peptide bond with the growing
peptide chain, and blocks further peptide elongation.  By linking puromycin to mRNA, a peptide-RNA fusion product resultsfrom the translation of the message linking the encoding mRNA with its peptide product.

Item

Catalog No.

Pack

Puromycin CPG

20-4040-01
20-4040-10
20-4140-41
20-4140-42
20-4140-13
20-4140-14

0.1g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole columns (Expedite)

N(CH 3)2

O
HN
DMTO

O

N

O

Pyrene-dU

DMTO

O

O

O

P

N(iPr)2O

CNEt

Perylene-dU

ON

NH O succinyl-lcaa-CPG

NO

O CNEt

N

DMTO

HN

O
O P N(iPr)2

N

N

H

NHCOCF 3

OCH 3

Puromycin CPG

128

LABELINGLABELING WITH METAL CHELATESREFERENCES

2,2’-Dipicolylamine Phosphoramidite has been discontinued.  This product was manufactured and developed by Syntrix
Biosystems Inc.  For further information, please contact:
Dean Y. Maeda, Ph.D., M.B.A.
Director, Chemistry and Preclinical Development
Syntrix Biosystems
215 Clay St NW Ste B5
Auburn, WA 98001
tel: 253-833-8009 ext. 23
fax: 253-833-8127
Dmaeda@syntrixbio.com(1) H. Asanuma, et al., Angew Chem Int
Ed, 2001, 40, 2671-2673.
(2) T. Takarada, et al., Chem Lett., 2001,
30, 732.
(3) H. Asanuma, X.G. Liang, T. Yoshida,
and M. Komiyama, Chembiochem,
2001, 2, 39-44.
(4) H. Asanuma, D. Matsunaga, and M.
Komiyama, NUCLEIC ACIDS SYMP SER(OXF), 2005, 49, 35.
(5) H. Asanuma, et al., Chembiochem,
2002, 3, 786.
(6) M. Liu, H. Asanuma, and M.
Komiyama, J. Amer. Chem. Soc., 2006 ,128, 1009.
(7) H. Asanuma, et al., Nature Protocols,
2007, 2, 203-212.

LABELING FOR PHOTO-REGULATION OF OLIGONUCLEOTIDES• Light does not introduce contaminants into the reaction system,• Excitation wavelength can be controlled through the design of the photo-responsive molecule, and• It is now straightforward to control irradiation time and/or local excitation.
When a photo-responsive molecule is directly attached to DNA as a receptor, photo-regulation of the bioprocess regulatedby that DNA molecule could, in principle, be achieved. Such photo-responsive DNA could also be used as a switch in a DNAbased nano-machine.  Professor Hiroyuki Asanuma and his group at the department of Molecular Design and Engineeringof the Graduate School of Engineering of the Nagoya University (Japan) have developed an efficient method to achieve thisgoal. They have attached azobenzene to DNA and made it photo-responsive1,2. Azobenzene is a typical photo-responsive
molecule that isomerizes from its planar trans-form to the non-planar cis-form after UV-light irradiation with a wavelength
between 300 nm and 400 nm (lmax is  around 330 nm). Interestingly, the system reverts from the cis-form to the trans-form
after further irradiation with visible light (wavelength over 400 nm). This process is completely reversible, and the azobenzene
group does not decompose or induce undesirable side reactions even on repeated trans-cis isomerization.  By introducing
azobenzenes into DNA through D-threoninol as a linker, Asanuma and co-workers succeeded in achieving photo-regulation of:

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)• Formation and dissociation of a DNA duplex3,4 and• Transcription by T7-RNA polymerase reaction5,6,7
Item

Catalog No.

Pack

Azobenzene Phosphoramidite

10-5800-95
10-5800-90
10-5800-02

50 µmole
100 µmole
0.25g

O

DMTO
N
N

N

DMTO

O

P

N(iPr)2

O

CNEt

H3 C

N

N
H

N

O
P

N(iPr)2O

CNEt

Azobenzene Phosphoramidite

2,2’-Dipicolylamine

129

MODIFICATION/LABELING

Photo-control, the use of ultraviolet or visible light to control a reaction, has a number of advantages over other external
stimuli:LABELINGQUENCHED AUTOLIGATION (QUAL) PROBESREFERENCES(1) Y. Yoshimura, and K. Fujimoto, Org
Lett, 2008, 10, 3227-30.
(2) K. Fujimoto, K. Konishi-Hiratsuka,
T. Sakamoto, and Y. Yoshimura,
ChemBioChem, 2010, 11, 1661-4.
(3) Y. Yoshimura, T. Ohtake, H. Okada, andK. Fujimoto, ChemBioChem, 2009, 10,1473-6.

CN

N
DMTO

O
O

P

N(iPr)2O

CNEt

3-Cyanovinylcarbazole

QUAL probes2 consist of two oligonucleotides, the first containing a nucleophilic group at the 3’-terminus, while the second
has an electrophilic group at the 5’-terminus.  When the probe pair finds the target, the oligos line up with the 3’-terminusof the first directly adjacent to the 5’-terminus of the second.  An autoligation reaction then takes place to combine the twooligos into a single probe.  As usual, the 3’ nucleophilic group is the 3-thiophosphate, easily prepared using 3’-phosphate
CPG with a sulfurizing step in the first cycle.  In this case, the electrophilic group is a 5’-dabsyl group, which is an excellent
leaving group as well as a fine quencher of fluorescence.  The second oligo, therefore, contains a fluorophore which isquenched by the dabsyl group.  A popular choice for fluorophore is fluorescein-dT but it is easy to imagine that a variety
of fluorophores could be attached to any of the commercially available amino-modified nucleoside phosphoramidites.

Item

Catalog No.

Pack

5’-Dabsyl-dT-CE Phosphoramidite

10-1532-90
10-1532-02

100 µmole
0.25g

LABELING WITH ULTRAFAST PHOTO CROSS-LINKER
When 3-cyanovinylcarbazole nucleoside (CNVK) is incorporated into an oligonucleotide, very rapid photo cross-linking to
the complementary strand can be induced at one wavelength and rapid reversal of the cross-link is possible at a second
wavelength.  Neither wavelength has the potential to cause significant DNA damage.  Irradiation of a duplex containing asingle incorporation of CNVK at 366 nm led to 100% cross-linking to thymine base in 1 second, although complete cross-linking
to cytosine takes 25 seconds.1  A 30 second irradiation time should cover all situations.  In addition, it was demonstrated thatthe purine bases were unreactive to cross-linking, allowing differentiation between pyrimidines and purines at the target
site.  The authors also determined the effect of sequence contexts around the CNVK site and demonstrated that the identity ofbases on either side of the cross-linking site has little effect on the reaction.  Once cross-linked, the UV melting temperatureof the duplex was raised by around 30 °C relative to the duplex before irradiation.  Complete reversal of the cross-link takes
place at 312 nm in 3 minutes.  This facile reversal reaction is, therefore, accomplished with no damage to normal DNA.
In a later publication, a further application of this cross-linking technique was investigated.2 When CNVK was cross-linked
with a dC residue in duplex DNA, heating at 90° C for 3.5 hours led to deamination of the cytosine base to form uracil in thecomplementary strand.  Reversal of the cross-link at 312 nm led to a DNA strand in which dC had been converted to dU.  
The authors showed that this transformation is specific for the dC residue opposite the CNVK and any further adjacent dC
residues are unaffected.  Similarly, the authors have shown that CNVK can be cross-linked to an adjacent RNA strand.3

Item

Cat. No.

3-Cyanovinylcarbazole Phosphoramidite(CNVK)

10-4960-95
10-4960-90
10-4960-02

Pack
50 µmole
100 µmole
0.25g
CN











N
DMTO

i 


5’-Dabsyl-dT

130

O
O

P

N(iPr)2O

CNEt

3-Cyanovinylcarbazole Phosphoramidite(CNVK)

RNA SUPPORTS
RNA SUPPORTS FOR 3’ MODIFICATION

Item

Catalog No.

Pack

Bz-A-RNA-CPG

20-3303-01
20-3303-02
20-3303-10
20-3403-41
20-3403-42
20-3403-13
20-3403-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3315-01
20-3315-02
20-3315-10
20-3415-41
20-3415-42
20-3415-13
20-3415-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3324-01
20-3324-02
20-3324-10
20-3424-41
20-3424-42
20-3424-13
20-3424-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3330-01
20-3330-02
20-3330-10
20-3430-41
20-3430-42
20-3430-13
20-3430-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole columns (ABI)
15 µmole column (Expedite)
Ac-C-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
Ac-G-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
U-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

NHBz
N
DMTO

N

N
O
O

OAc

succinyl-CPG

Bz-A-CPG

O

NHAc
N

DMTO

O

N
O

O

OAc

succinyl-CPG

Ac-C-CPG

AcHN

HN

N

N

DMTO

Ac = Acetyl
Bz = Benzoyl
CNEt = Cyanoethyl
CPG = Controlled Pore Glass
DMT = 4,4’-Dimethoxytrityl

O
N

HN

N

ABBREVIATIONSRNA AND 2’-OMe-RNA

Glen Research offers RNA supports in which protected ribonucleosides are attached to CPG.  With 5’-DMT protection, andall other protecting groups base-labile, the use of these supports is identical to DNA supports.  These supports are suitablefor use in producing oligodeoxynucleotides modified at the 3’-terminus or oligoribonucleotides.  ABI-style columns aresupplied unless otherwise requested (see note box).

DMTO

O

O

OAc

succinyl-CPG

Ac-G-CPG

O

N
O

O

OAc

succinyl-CPG

U-CPG

131

RNA SYNTHESISTOM-PROTECTED RNA PHOSPHORAMIDITESINTELLECTUAL PROPERTY
2'- O

O

Si

TOM-Protecting-Group™
TOM-Protecting-Group is a trademark
of QIAGEN.

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

RNA synthesis using monomers containing the 2’-O-TriisopropylsilylOxyMethyl (TOM) group (TOM-Protecting-Group™)
is characterized by very high coupling efficiency along with fast, simple deprotection.  High coupling efficiency is achieved
because the TOM-Protecting-Group exhibits lower steric hindrance than the 2’-O-t-butyldimethylsilyl (TBDMS) groupused in our alternative RNA monomers.  Fast and reliable deprotection is achieved using methylamine in ethanol/water atroom temperature.  A further feature of the TOM-Protecting-Group is that during basic steps it can not undergo 2’ to 3’
migration.  This migration under basic conditions leads to non-biologically active 2’-5’ linkages when using the TBDMS group.  
These features allow the TOM-Protected monomers to produce longer oligonucleotides.  TOM-Protected RNA monomers
are also fully compatible with minor bases with 2’-O-TBDMS protection.

Item

Catalog No.

Pack

A-TOM-CE Phosphoramidite

10-3004-02
10-3004-05
10-3004-10

0.25g
0.5g
1.0g

10-3014-02
10-3014-05
10-3014-10

0.25g
0.5g
1.0g

G-TOM-CE Phosphoramidite

10-3024-02
10-3024-05
10-3024-10

0.25g
0.5g
1.0g

U-TOM-CE Phosphoramidite

10-3034-02
10-3034-05
10-3034-10

0.25g
0.5g
1.0g

Item

Catalog No.

Pack

Ac-A-RNA-CPG

20-3304-01
20-3304-02
20-3304-10
20-3404-41
20-3404-42
20-3404-13
20-3404-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1­
C-TOM-CE Phosphoramidite

RNA SUPPORTS FOR TOM RNA SYNTHESIS

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

NHAc
N
DMTO

N

N
O

DMTO

O

O
N

HN

N
N
O

AcHN
DMTO

HN

N

N
O

DMTO

O

N
O

OTOM
O P N(iPr)2

OTOM
O P N(iPr)2

OTOM
O P N(iPr)2

OTOM
O P N(iPr)2

A-TOM

C-TOM

G-TOM

U-TOM

O CNEt

132

O

NHAc
N

O CNEtO CNEtO CNEtRNA SYNTHESIS

Item

Catalog No.

Pack

Ac-C-RNA-CPG

20-3315-01
20-3315-02
20-3315-10
20-3415-41
20-3415-42
20-3415-13
20-3415-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3324-01
20-3324-02
20-3324-10
20-3424-41
20-3424-42
20-3424-13
20-3424-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3330-01
20-3330-02
20-3330-10
20-3430-41
20-3430-42
20-3430-13
20-3430-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
Ac-G-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
U-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)

RNA AND 2’-OMe-RNA

RNA SUPPORTS FOR TOM RNA SYNTHESIS (CONT.)133

RNA SYNTHESISTBDMS-PROTECTED RNA PHOSPHORAMIDITESABBREVIATIONS
Bz = Benzoyl
CNEt = Cyanoethyl
CPG = Controlled Pore Glass
dmf = Dimethylformamidine
DMT = 4,4’-Dimethoxytrityl
iPr = Isopropyl
lcaa = long chain alkylamino
Pac = Phenoxyacetyl
PhOAc = Phenoxyacetyl
TBDMS = t-Butyl-dimethylsilyl

INSTRUMENT TYPES
Glen Research packages thesemonomers in a variety of industrystandard vials and bottles.  Pleaseprovide the exact specification of thebottle required prior to receiving aquotation.

Glen Research CE (ß-cyanoethyl) Phosphoramidites for RNA synthesis are produced and packaged to ensure the highest
performance on commercial synthesizers. Every batch is accompanied by a Certificate of Analysis and an HPLC trace, showing
the results of our QC testing. RNA Phosphoramidites are synthesis-tested with a minimum coupling efficiency of 97%.
Glen Research RNA monomers are packaged in industry standard vials which are specially cleaned to eliminate particulatecontamination. These monomers are available in a variety of packs, including high throughput (HT) and low cost (LC).
An UltraMild set is also available for situations where sensitive bases are in use. Dmf-G (10-3029) has been discontinued
and may be substituted with Ac-G (10-3025).

Item

Catalog No.

Pack

Bz-A-CE Phosphoramidite				
­Ac-C-CE Phosphoramidite				

10-3003-02
10-3003-05
10-3003-10

0.25g
0.5g
1.0g

10-3015-02
10-3015-05
10-3015-10

0.25g
0.5g
1.0g

Ac-G-CE Phosphoramidite				

10-3025-02
10-3025-05
10-3025-10

0.25g
0.5g
1.0g

U-CE Phosphoramidite				

10-3030-02
10-3030-05
10-3030-10

0.25g
0.5g
1.0g

RNA PHOSPHORAMIDITES - SPECIAL PACKAGING
We offer our high quality DNA phosphoramidites specifically packaged for high throughput and large-scale synthesis
customers. These customers normally require high quality materials produced under the guidelines of a validated quality
management system while still being priced aggressively. These products include the usual Glen Research certification andguarantees and they are available in larger packs or in bulk. The core catalog numbers for regular DNA phosphoramidites
are shown below. For these products, please request a quote.

Item

Catalog No.

Bz-A-CE Phosphoramidite
Ac-C-CE Phosphoramidite
Ac-G-CE Phosphoramidite
U-CE Phosphoramidite

10-3003-SP
10-3015-SP
10-3025-SP
10-3030-SP

DMTO

N

N
O

O

OTBDMSP N(iPr)2

134

O

N

N

N

O

NHAc

NHBz

DMTO

O

N

HN

N
AcHN

O
OTBDMSP

N(iPr)2

O CNEtO CNEtBz-A-CE Phosphoramidite

Ac-C-CE Phosphoramidite

N

N

DMTO

O

HN
DMTO

O

N
O

O

O

P

OTBDMS
N(iPr)2

O-CNEtAc-G-CE PhosphoramiditeO

OTBDMSP

N(iPr)2

O CNEtU-CE Phosphoramidite

RNA SYNTHESISULTRAMILD TBDMS RNA PHOSPHORAMIDITESOTHER INSTRUMENT TYPES

Item

Catalog No.

Pack

Pac-A-CE Phosphoramidite

10-3000-02
10-3000-05
10-3000-10

0.25g
0.5g
1.0g

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

10-3015-02
10-3015-05
10-3015-10

0.25g
0.5g
1.0g

Monomers
For Instrument type

Add

10-3021-02
10-3021-05
10-3021-10

0.25g
0.5g
1.0g

Expedite
MerMadeE
M

Columns
For Instrument type

Add

10-3030-02
10-3030-05
10-3030-10

0.25g
0.5g
1.0g

Expedite
Applied Biosystems 3900
MerMadeE
A
M­
Ac-C-CE Phosphoramidite

iPr-Pac-G-CE Phosphoramidite

U-CE Phosphoramidite

TBDMS RNA SUPPORTS(Please inquire for availability of vials andcolumns for other instrument types.)

Item

Catalog No.

Pack

Pac-A-RNA-CPG

20-3300-01
20-3300-02
20-3300-10
20-3400-41
20-3400-42
20-3400-13
20-3400-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3303-01
20-3303-02
20-3303-10
20-3403-41
20-3403-42
20-3403-13
20-3403-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)Bz-A-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
NHAcOPh

DMTO

NHAc

N

N

N

N

N

DMTO

O

O

OTBDMSP

N(iPr)2

O CNEtPac-A-CE Phosphoramidite

O

O
P

O

O
N

HN
N

O

iPr-PhOAc HN
DMTO

N

N
O

HN
DMTO

O

N
O

OTBDMSOOTBDMSOOTBDMS

N(iPr)2

P

N(iPr)2

P

N(iPr)2

O CNEtAc-C-CE Phosphoramidite

RNA AND 2’-OMe-RNA

ABI-style columns are supplied for 1 µmole and 0.2 µmole scales unless otherwise requested (see note box).

O CNEt

iPr-Pac-G-CE Phosphoramidite

O CNEtU-CE Phosphoramidite

135

RNA SYNTHESISTBDMS RNA SUPPORTS (CONT.)OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

Item

Catalog No.

Pack

Ac-C-RNA-CPG

20-3315-01
20-3315-02
20-3315-10
20-3415-41
20-3415-42
20-3415-13
20-3415-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3321-01
20-3321-02
20-3321-10
20-3421-41
20-3421-42
20-3421-13
20-3421-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3324-01
20-3324-02
20-3324-10
20-3424-41
20-3424-42
20-3424-13
20-3424-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3330-01
20-3330-02
20-3330-10
20-3430-41
20-3430-42
20-3430-13
20-3430-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

Catalog No.

Pack

40-4210-52
40-4210-57

200mL
450mL

40-4212-52
40-4212-57

200mL
450mL

60-4600-30
60-4600-52
60-4600-57

30mL
200mL
450mL

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
iPr-Pac-G-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
Ac-G-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)
U-RNA-CPG

1 µmole columns
0.2 µmole columns
10 µmole column (ABI)
15 µmole column (Expedite)ULTRAMILD SOLVENTS/REAGENTS
Item
Cap Mix A
THF/Pyridine/Pac2O  
(Applied Biosystems)		
THF/Pac2O   
(Expedite)
Deprotection Solution
0.05M Potassium Carbonate in Methanol

136

MINOR RNA BASESMINOR RNA PHOSPHORAMIDITES (TOM PROTECTED)
Glen Research offers minor RNA phosphoramidites with either TOM or TBDMS protecting groups.  4-Thio-U, 5-MethylCytidine, and 2-Amino-Adenosine are useful for analyzing RNA structure and activity relationships, for example, in ribozyme
studies.

RELATED
Minor TBDMS monomers.......139
Pyrrolo-CTP...............................142
rSpacer TBDMS........................140

Pyrrolo-C is a fluorescent nucleoside whose fluorescence is sensitive to its environment and is ideal for probing RNA structure.  
It base-pairs as a normal C nucleotide.  It is highly fluorescent and its excitation and emission are well suited to the red ofmost fluorescent nucleotide analogs, which eliminates or reduces background fluorescence from proteins.  Pyrrolo-CTP
has potential uses in biological assay development.
rSpacer is used to introduce an abasic site to an RNA sequence.  The TOM protected version has been discontinued and is
replaced with the TBDMS version.
The protecting scheme for 2,6-Diaminopurine has been changed and the original product (10-3084) has been replacedwith the optimized product (10-3085) below.

Catalog No.

Pack

4-Thio-U-TOM-CE Phosphoramidite

10-3052-95
10-3052-90
10-3052-02

50 µmole
100 µmole
0.25g

5-Me-C-TOM-CE Phosphoramidite

10-3064-95
10-3064-90
10-3064-02

50 µmole
100 µmole
0.25g

2,6-Diaminopurine-TOM-CE Phosphoramidite(2-amino-A)
                                                          10-3085-95
10-3085-90
10-3085-02

50 µmole
100 µmole
0.25g

RNA AND 2’-OMe-RNA

Item

CN
S

NHAc

N
N

O
DMTO

DMTO

O
OTOM
O

P

N(iPr)2

O

CNEt

4-Thio-U-TOM

O

NHiBu

Me

N
N
O

OTOM
O P N(iPr)2
O CNEt

5-Me-C-TOM

N

N
MeOAcHN

N

N

DMTO

O

O

P
O

OTOM

N(iPr)2CNEt

2,6-diaminopurine-TOM

137

MINOR RNA BASESMINOR RNA PHOSPHORAMIDITES (TOM PROTECTED) (CONT.)
RELATED
Pyrrolo-dC...................................74
Pyrrolo-CTP...............................142

Item

Catalog No.

Pack

Pyrrolo-C-TOM-CE Phosphoramidite

10-3017-95
10-3017-90
10-3017-02

50 µmole
100 µmole
0.25g

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

RNA SEQUENCE MODIFIER (TOM PROTECTED)

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Item

Catalog No.

Pack

Expedite
Applied Biosystems 3900
MerMadeE
A
M

Amino-Modifier C6-U Phosphoramidite

10-3039-95
10-3039-90
10-3039-02

50 µmole
100 µmole
0.25g

Amino-Modifier C6-U has been added to the growing family of sequence modifiers and we envisage applications in RNA
structural studies as well as for labeling siRNA to probe uptake and cellular distribution.

(Please inquire for availability of vials andcolumns for other instrument types.)

O

HN
HN

N
DMTO

O

O

N

OTOM
O P N(iPr)2
O CNEtPyrrolo-C-TOM

138

DMTO

DMTO

O
OTOM
O P N(iPr)2
O CNEtrSpacer

O

O

O
NH

N
O
OTOM

O P N(iPr)2
O CNEtAmino-Modifier C6-U

NHCCF 3MINOR RNA BASESMINOR RNA PHOSPHORAMIDITES (TBDMS PROTECTED)
RELATED

Inosine and 5-Methyl-Uridine are useful for analyzing RNA structure and activity relationships.   5-Bromo-Uridine and
5-Iodo-Uridine have been used for crystallography studies and cross-linking experiments.  6-Thioguanosine (6-thio-G) has
applications in ribozyme and siRNA research, as well as in RNA-protein interactions.  The removal of the silyl protecting
group without interfering with the sulfur is critical.  This is removed1 cleanly by triethylamine trihydrofluoride in DMSO
but t-butylammonium fluoride (TBAF) leads to degradation of the thio-nucleotide analogue and should not be used.  
2-Aminopurine riboside is useful for analyzing RNA structure and activity relationships, for example, in ribozyme studies.
Catalog No.

Pack

I-CE Phosphoramidite

10-3040-95
10-3040-90
10-3040-02

50 µmole
100 µmole
0.25g

5-Me-U-CE Phosphoramidite     (T)

10-3050-95
10-3050-90
10-3050-02

50 µmole
100 µmole
0.25g

Br-U-CE Phosphoramidite

10-3090-95
10-3090-90
10-3090-02

50 µmole
100 µmole
0.25g

I-U-CE Phosphoramidite

10-3091-95
10-3091-90
10-3091-02

50 µmole
100 µmole
0.25g

6-Thio-G-CE Phosphoramidite

10-3072-95
10-3072-90
10-3072-02

50 µmole
100 µmole
0.25g

2-Aminopurine-CE Phosphoramidite                                                                 

10-3070-95
10-3070-90
10-3070-02

50 µmole
100 µmole
0.25g

REFERENCES(1) C.J. Adams, J.B. Murray, M.A.
Farrow, J.R.P. Arnold, and P.G.
Stockley, Tetrahedron Lett., 1995,
36, 5421-5424.
(2) D.A. Berry, et al., Tetrahedron Lett,
2004, 45, 2457-2461.

RNA AND 2’-OMe-RNA

Item

Minor TOM monomers...........137

CN
O

O
HN
DMTO

N

N

HN

N

O

O

DMTO

O

CH 3
N
DMTO

O

O

OTBDMSOTBDMSOO P N(iPr)2P

O CNEtO CNEt

5-Me-UNOO P N(iPr)2

InosineOBr

HN

OTBDMS

N(iPr)2

O CNEt

Br-U

S

DMTO

O

O

N

O

OTBDMSP

N(iPr)2

O CNEt

I-U

N

N

I

HN

iBuHN
DMTO

N

N

O
N
H

O

N

N

N

N

DMTO

O

OTBDMSO P N(iPr)2
O CNEt6-Thio-GOPOTBDMS
N(iPr)2O

CNEt

2-Aminopurine

139

MINOR RNA BASESMINOR RNA (TBDMS PROTECTED) (CONT.)OTHER INSTRUMENT TYPES

8-Aza-7-deaza-Adenosine is an isomer of Adenosine with virtually identical electron density.  The N7 nitrogen is not available
for hydrogen bonding.  

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M

Ribozyme activity is substantially affected by the substitution of modified pyrimidine bases.  Zebularine (pyrimidin-2-one
ribonucleoside) may be regarded as a Cytidine derivative lacking the exocyclic amino group.  Zebularine and Pyridin-2-one
Ribonucleoside, the 3-deaza analogue of Zebularine, are prime candidates for use in evaluating ribozyme activity andfunction.  It should be noted that Zebularine is mildly fluorescent, absorbing at 298 nm and emitting at 367 nm.
PseudoUridine is one of the most common modified nucleosides found in RNA.  The availability of a phosphoramidite willallow detailed research into the effects of this modified base on RNA structure and activity.
rSpacer is used to introduce an abasic site to an RNA sequence.

(Please inquire for availability of vials andcolumns for other instrument types.)

Item

Catalog No.

Pack

Zebularine-CE Phosphoramidite

10-3011-95
10-3011-90
10-3011-02

50 µmole
100 µmole
0.25g

Pyridin-2-one-CE Phosphoramidite

10-3012

Discontinued

PseudoUridine-CE Phosphoramidite

10-3055-95
10-3055-90
10-3055-02

50 µmole
100 µmole
0.25g

8-Aza-7-deaza-A-CE Phosphoramidite

10-3083

Discontinued

rSpacer TBDMS CE Phosphoramidite

10-3915-95
10-3915-90
10-3915-02

50 µmole
100 µmole
0.25g

N

N

N

N

O
HN

N
O

DMTO

O

O

P
O

N

OTBDMS
N(iPr)2
CNEt

Zebularine

140

O

DMTO

O

O

P
O

N

OTBDMS
N(iPr)2
CNEt

Pyridin-2-one

DMTO

DMTO

O

O

P
O

N

NH

O

OTBDMS
N(iPr)2
CNEt

PseudoUridine

N
DMTO

O

O

O

P
O

OTBDMS
N(iPr)2
CNEt

8-Aza-7-deaza-A

OTBDMSOP

N(iPr)2O

CNEt

rSpacer TBDMSMINOR RNA BASESMINOR RNA (TBDMS PROTECTED) (CONT.)
Methylation of adenosine at position 1 produces a drastic functional change in the nucleobase. 1-Methyladenosine (pKa8.25) is a much stronger base than adenosine (pKa 3.5).  N-1 methylation excludes participation of the adenine base incanonical Watson–Crick base pairing and provides a positive charge to the nucleobase.  This modification also alters thehydrophobicity of the base, the stacking properties, the ordering of water molecules and the chelation properties. The base
may become involved in non-canonical hydrogen bonding, in electrostatic interactions and, in general, it may contribute to
the conformational dynamics of the tRNA.
In the central dogma of molecular biology, genetic information flows from DNA to RNA and then to protein. Reversible
epigenetic modifications on genomic DNA and histone have been known to substantially regulate gene expression. On theother hand, there exists more than 100 naturally occurring chemical modifications in RNA; however, the functions of these
RNA modifications are largely unknown. Whether some of these modifications in RNA can be reversed and could impact
gene expression in the central dogma was unknown until the recent discovery of N6-methyladenosine (N6-Me-A) as the firstexample of reversible RNA methylation.1  We offer the N6-Me-A RNA monomer with a phenoxyacetyl protecting group to
minimize potential branching.  We have shown N6-Me-A-CE Phosphoramidite to be completely compatible with all popular
RNA synthesis and deprotection methods, from UltraMild to the most popular procedure using AMA for deprotection.

Item

Catalog No.

Pack

1-Me-A-CE Phosphoramidite

10-3501-95
10-3501-90
10-3501-02

50 µmole
100 µmole
0.25g

N6-Me-A-CE Phosphoramidite

10-3005-95
10-3005-90
10-3005-02

50 µmole
100 µmole
0.25g

REFERENCE(1) Y. Fu, D. Dominissini, G. Rechavi, and C.
He, Nat Rev Genet, 2014, 15, 293-306.

RELATED
5-Me-C......................................137
Pseudouridine..........................140

Item

Catalog No.

Pack

1-Me-Pseudouridine Phosphoramidite

10-3056-95
10-3056-90
10-3056-02

50 µmole
100 µmole
0.25g

RNA AND 2’-OMe-RNA

RNA methylation occurs in a large selection of RNA nucleosides and this post transcriptional modification of RNA, carried out
by a variety of RNA methyltransferases, appears in a wide variety of RNA species - including tRNA, mRNA, miRNA and RNA
viruses.  Over 90 methylated nucleosides have been found in tRNA and these play many significant roles in tRNA structure.  
In addition, methylation appears to mark the tRNA as mature, preventing its degradation as well as directing localization
within the cell. mRNA, modified with 1-methylpseudouridine (1-Me-Y) alone or in combination with 5-methylcytidine(5-Me-C), significantly increases protein expression in cells and mouse models.  1-Me-Y is also a modified nucleobase thatcan greatly enhance the properties of mRNA by reducing immunogenicity and increasing stability.  

O





PhO



CH3

N

P

N(iPr)2

O

CNEt

1-Me-A

N6-Me-ACH3O

OTBDMSOL 

N

O

DMTO

O

 

 

HN

N

N
DMTO



O

N

N

O

P
O

OTBDMS
N(iPr)2
CNEt

1-Me-Pseudouridine141

MINOR RNA BASESMINOR RNA (TBDMS PROTECTED) (CONT.)REFERENCE(1) Füchtbauer, A.F., Preus, S., Börjesson,
K., McPhee, S.A., Lilley D.M.J.,
Wilhelmsson, L.M., Sci. Rep., 2017, 7,
2393.

INTELLECTUAL PROPERTY

The bright fluorescent tricyclic cytosine analogues tC and tCO stand out among fluorescent bases due to their virtuallyunquenched fluorescence inside single- or double-stranded DNA. Until recently, this family of tricyclic cytosines had only
been studied and used in DNA contexts and, importantly, introduced as possible donors of the first DNA base analogue
FRET-pair with tCnitro. Fluorescent base analogues for RNA are limited in number compared to their DNA counterparts.
To facilitate the application of such analogues, characterization of their structural and dynamics behavior in RNA comparedto the corresponding natural nucleoside is important.   We now introduce the tCO ribonucleoside, which has been
incorprated into a range of RNA sequences, where it was shown to be a very potent and useful fluorophore in this context.1
Glen Research offers this useful fluorescent ribonucleoside analogue in cooperation with ModyBase HB.

These products are offered incollaboration with ModyBase HB.

RELATEDtC ...............................................76
Pyrrolo-dC...................................74
Pyrrolo-C...................................138

Item

Catalog No.

Pack

Ribo-tCO-CE Phosphoramidite

10-3517-95
10-3517-90
10-3517-02

50 µmole
100 µmole
0.25g

O

MINOR RNA TRIPHOSPHATES
Pyrrolo-dC is a fluorescent nucleoside that codes as dC and base pairs efficiently with dG.  Preliminary evidence indicatesthat pyrrolo-dC triphosphate is an excellent substrate for Taq, Pfu and Vent polymerases and is incorporated specifically
opposite dG. Pyrrolo-dCTP has been available for some time and is in use in biological assays.  Pyrrolo-CTP is a fluorescentribonucleotide with fluorescence exquisitely sensitive to its environment and is of great interest for RNA structural research.  
The pyrrolo-C project is a joint development by Berry and Associates, Inc. and Glen Research Corporation.

Item

Catalog No.

Pack

Pyrrolo-CTP
10mM

81-3017-01

Discontinued

HN
O

N
N

O
DMTO

O

O
OTBDMSOP

N(iPr)2O

CNEt

Ribo-tC°

142

NH

HO

P

O
P

N

O
P

O
O
O
OH OH OH

O

O

N

OH OH

Pyrrolo-CTP

CH 3

2’-OME-RNA SYNTHESIS
2’-OME-RNA PHOSPHORAMIDITES

ItemCatalog No.

Pack

2’-OMe-A-CE Phosphoramidite

10-3100-90
10-3100-02
10-3100-05
10-3100-10

100 µmole
0.25g
0.5g
1.0g

10-3115-90
10-3115-02
10-3115-05
10-3115-10

100 µmole
0.25g
0.5g
1.0g

2’-OMe-iBu-G-CE Phosphoramidite

10-3120-90
10-3120-02
10-3120-05
10-3120-10

100 µmole
0.25g
0.5g
1.0g

2’-OMe-G-CE Phosphoramidite

10-3121-90
10-3121-02
10-3121-05
10-3121-10

100 µmole
0.25g
0.5g
1.0g

2’-OMe-U-CE Phosphoramidite

10-3130-90
10-3130-02
10-3130-05
10-3130-10

100 µmole
0.25g
0.5g
1.0g

2’-OMe-Ac-C-CE Phosphoramidite

NHBz

NHBz
N

N
DMTO

N

N
O

NHAc

N
DMTO

N

O

N
O

DMTO

O

O

O
N

HN

N
O

O

N
H
DMTO

N

N

(Me) 2N

N
DMTO

DMTO

O

O

O

OMe

O

OMe

O

OMe

O

OMe

O

OMe

O

OMe

N(iPr)2

P

N(iPr)2

P

N(iPr)2

P

N(iPr)2

P

N(iPr)2

P

N(iPr)2O

CNEt

O CNEt2’-OMe-C

O CNEt2’-OMe-Ac-C

2’-OMe-iBu-G

O CNEt2’-OMe-G

E
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)NP

O CNEtAdd

Expedite
MerMadeOO

2’-OMe-A

Monomers
For Instrument type

HN

N

N

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

O

N

HN

OTHER INSTRUMENT TYPESRNA AND 2’-OMe-RNA

Glen Research 2’-OMe-RNA CE (ß-cyanoethyl) Phosphoramidites are designed to produce synthetic oligonucleotides
containing nuclease resistant 2’-O-methyl ribonucleotide linkages.  Deprotection, isolation and handling of 2’-O-methyl
oligonucleotides are identical to the procedures for oligodeoxynucleotides.

O CNEt2’-OMe-U143

2’-OME-RNA SYNTHESISULTRAMILD 2’-OME-RNA
The use of UltraMild monomers in oligonucleotide synthesis has allowed very sensitive dyes like TAMRA, HEX and Cy5 to be
used virtually routinely.  The DNA and RNA monomers are currently available and we also provide this set of 2’-OMe-RNAmonomers.  In our version of this chemistry, we use as protecting groups phenoxyacetyl (Pac) for A, acetyl (Ac) for C, andisopropyl-phenoxyacetyl (iPr-Pac) for G.
It has become clear that acetic anhydride in the conventional capping mix can cause transamidation in situations where anamine protecting group is quite labile.   This leads to acetyl protection on the amino group that may be slow to be removed.  
Consequently, if many dG residues are included in the oligonucleotide, we recommend the use of phenoxyacetic anhydride(Pac2O) in Cap A.  This modification removes the possibility of exchange of the iPr-Pac protecting group on the dG withacetate from the acetic anhydride capping mix.

Item

Catalog No.

Pack

2’-OMe-Pac-A-CE Phosphoramidite

10-3601-02
10-3601-05
10-3601-10

0.25g
0.5g
1.0g

2’-OMe-Ac-C-CE Phosphoramidite

10-3115-02
10-3115-05
10-3115-10

0.25g
0.5g
1.0g

2’-OMe-iPr-Pac-G-CE Phosphoramidite

10-3621-02
10-3621-05
10-3621-10

0.25g
0.5g
1.0g

40-4210-52
40-4210-57

200mL
450mL

40-4212-52
40-4212-57

200mL
450mL

60-4600-30
60-4600-52
60-4600-57

30mL
200mL
450mL

ULTRAMILD SOLVENTS/REAGENTS
Cap Mix A
THF/Pyridine/Pac2O  
(Applied Biosystems)		
THF/Pac2O   
(Expedite)
Deprotection Solution
0.05M Potassium Carbonate in Methanol

NHAc
NHAcOPh
N

N
DMTO

N

N

DMTO

O

O
N

HN
N

O

O

iPr-PhOAcHN
DMTO

N

N
O

O

OMe

P

O CNEtN(iPr)2

O CNEtOMe
O P N(iPr)22’-OMe-Pac-A

2’-OMe-Ac-C

2’-OMe-iPr-Pac-GOMe
O P N(iPr)2

144

N

O CNEt2’-OME-RNA SYNTHESIS
2’-OME-RNA SUPPORTS

OTHER INSTRUMENT TYPES

ABI-style columns are supplied for 1 µmole and 0.2 µmole scales unless otherwise requested (see note box).  

Item

Catalog No.

Pack

2’-OMe-A-RNA-CPG

20-3600-01
20-3600-02
20-3600-10
20-3700-41
20-3700-42
20-3700-13
20-3700-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3610-01

Discontinued

1  µmole columns
0.2  µmole columns
10  µmole column (ABI)
15  µmole column (Expedite)
2’-OMe-C-RNA-CPG

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M

2’-OMe-Ac-C-RNA-CPG

1  µmole columns
0.2  µmole columns
10  µmole column (ABI)
15  µmole column (Expedite)
2’-OMe-G-RNA-CPG

1  µmole columns
0.2  µmole columns
10  µmole column (ABI)
15  µmole column (Expedite)
2’-OMe-U-RNA-CPG

1  µmole columns
0.2  µmole columns
10  µmole column (ABI)
15  µmole column (Expedite)20-3615-01
20-3615-02
20-3615-10
20-3715-41
20-3715-42
20-3715-13
20-3715-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3621-01
20-3621-02
20-3621-10
20-3721-41
20-3721-42
20-3721-13
20-3721-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

20-3630-01
20-3630-02
20-3630-10
20-3730-41
20-3730-42
20-3730-13
20-3730-14

0.1g
0.25g
1.0g
Pack of 4
Pack of 4
Pack of 1
Pack of 1

RNA AND 2’-OMe-RNA(Please inquire for availability of vials andcolumns for other instrument types.)145

2’-OME-RNA SYNTHESISMINOR 2’-OME-RNA PHOSPHORAMIDITESOTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeEA
M

To aid in the evaluation of the structures of 2’-OMe-RNA complexes, we offer the CE phosphoramidites listed below.  
2’-OMe-T is useful in triplex studies while the 2-aminopurine derivative may be tested in ribozyme studies.  By supporting an
additional hydrogen bond, 2,6-diaminopurine (2-amino-adenosine) binds more strongly with uridine than does adenosine.  
Oligonucleotides containing 2’-OMe-5-Me-C and 2’-OMe-I would be of interest to researchers involved in triplex and antisensestudies using 2’-OMe-RNA.  The uses of 2’-OMe-5-bromo-U phosphoramidite range from crystallographic studies due to theheavy atom to cross-linking because of its photolability.  5-Fluoro-pyrimidine nucleosides have been useful as therapeutic
agents and their effect on the structure and activity of oligonucleotides may be examined using the 2’-OMe-RNA derivatives.    
ABI-style vials are supplied unless otherwise requested (see note box).

(Please inquire for availability of vials andcolumns for other instrument types.)

O

N

N

HN

N

N

DMTO

Catalog No.

Pack

2’-OMe-2-Aminopurine-CE Phosphoramidite

10-3123

Discontinued

2’-OMe-2,6-DiaminopurineCE Phosphoramidite(2-amino-A)

10-3124-95
10-3124-90
10-3124-02

50 µmole
100 µmole
0.25g

2’-OMe-5-Me-U-CE Phosphoramidite(2’-OMe-T)

10-3131-90
10-3131-02

100 µmole
0.25g

2’-OMe-I-CE Phosphoramidite

10-3140-90
10-3140-02

100 µmole
0.25g

2’-OMe-5-Me-C-CE Phosphoramidite

10-3160-90
10-3160-02

100 µmole
0.25g

2’-OMe-5-Br-U-CE Phosphoramidite

10-3190-90
10-3190-02

100 µmole
0.25g

2’-OMe-5-F-U-CE Phosphoramidite

10-3132

Discontinued

NMe 2

N

iBuHN

Item

DMTO

O

O

N
O

O

OMe

O

P

N(iPr)2

O CNEtP N(iPr)2O CNEt2’-OMe-2-amino-A

2’-OMe-5-Me-U

146

OMe

CH 3

N

HN
DMTO

N

N

N

O

DMTO

O

CH3

N

O

O

O

NHAc

O

Br

HN
DMTO

O

N
O

F

N
DMTO

O

N
O

OMe

O

OMe

O

OMe

O

OMe

P N(iPr)2

P

N(iPr)2

P

N(iPr)2

P

O

CNEt

N(iPr)2OO CNEt2’-OMe-I

2’-OMe-5-Me-C

O CNEt2’-OMe-5-Br-U

NMe 2

N
N
DMTO

O

N
O

O

OMe

P N(iPr)2O CNEtO CNEt2’-OMe-TMP-5-F-U

2’-OMe-3-deaza-5-aza-C

2’-OME-RNA SYNTHESIS
2’-OME-THIOPHOSPHORAMIDITESOTHER INSTRUMENT TYPESThe phosphorodithioate linkage (PS2) is both achiral and essentially resistant to nucleases. Previous studies have shown
very interesting results which include observations that DNA with PS2 linkages activates RNase H in vitro, strongly inhibits
human immunodeficiency virus (HIV) reverse transcriptase, induces B-cell proliferation and differentiation, and is completely
resistant to hydrolysis by various nucleases.  2’-OMe- RNA Thiophosphoramidites are RNA monomers designed to produce
oligos combining the PS2 linkage with the 2’-O-methyl ribose modification.  These PS2-modified RNA oligos have potential
for use in siRNAs and dithiophosphate aptamers (thioaptamers).  

All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Item

Catalog No.

Pack

Expedite
MerMadeE
M

2’-OMe-A-Thiophosphoramidite

10-3170-90
10-3170-02

100 µmole
0.25g

Columns
For Instrument type

Add

2’-OMe-C-Thiophosphoramidite

10-3171-90
10-3171-02

100 µmole
0.25g

Expedite
Applied Biosystems 3900
MerMadeE
A
M

2’-OMe-G-Thiophosphoramidite

10-3172-90
10-3172-02

100 µmole
0.25g

2’-OMe-U-Thiophosphoramidite

10-3173-90
10-3173-02

100 µmole
0.25g

RNA AND 2’-OMe-RNA(Please inquire for availability of vials andcolumns for other instrument types.)

NHBz

O
O
N P

O

O
N P

2'-OMe-A-Thiophosphoramidite

OMe

O

O
N P

OMe

O

O

O

SCH2CH2S C

N P

2'-OMe-G-Thiophosphoramidite

N

O

DMTO

O

SCH2CH2S C

2'-OMe-C-Thiophosphoramidite

HN

N

N

DMTO

O

SCH2CH2S C

OMe

iBuHN

N

O

DMTO

O

N

HN

N

N

N
DMTO

O

NHAc
N

N

OMe

O

SCH2CH2S C

2'-OMe-U-Thiophosphoramidite147

2’-MOE-RNA PHOSPHORMIDITES
2’-MOE RNA PHOSPHORAMIDITESOTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Like the very similar 2’-OMe backbone, the 2’-O-methoxyethyl-RNA (2’-MOE) backbone provides enhanced duplex stability,
significant nuclease resistance and relatively low toxicity. As a result, 2’-MOE has been an attractive backbone for many
therapeutic candidates, several of which have been approved by the FDA. These drugs have included 1) 2’-MOE/DNA
chimeras to facilitate RNase H cleavage of target RNA sequences as well as 2) steric blocking oligonucleotides to alter the
splicing of mRNA. The standard 2’-MOE nucleotides are A, 5-Me-C, G and 5-Me-U.
ABI-style vials are supplied unless otherwise requested (see note box).

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMade

E
A
M

Item

Catalog No.

Pack

A-2'-MOE-Phosphoramidite

10-3200-05
10-3200-10
10-3200-20

0.5g
1.0g
2.0g

5-Me-C-2'-MOE-Phosphoramidite

10-3211-05
10-3211-10
10-3211-20

0.5g
1.0g
2.0g

G-2'-MOE-Phosphoramidite

10-3220-05
10-3220-10
10-3220-20

0.5g
1.0g
2.0g

5-Me-U-2'-MOE-Phosphoramidite

10-3231-05
10-3231-10
10-3231-20

0.5g
1.0g
2.0g

(Please inquire for availability of vials andcolumns for other instrument types.)

A-2'-MOE

148

5-Me-C-2'-MOE

G-2'-MOE

5-Me-U-2'-MOE

2’-F RNA SYNTHESIS
2’-F-RNA PHOSPHORAMIDITES
2’-Deoxy-2’-fluoro-nucleosides adopt an RNA-type sugar conformation, presumably due to the high electronegativity offluorine.  Because of this sugar conformation, RNA duplexes (A-form) are generally more thermodynamically stable thanDNA duplexes (B-form).  As expected, the addition of 2’-F-RNA residues to oligodeoxynucleotides progressively increases
the thermal stability of their duplexes with RNA.  The stabilization is additive at approximately 2° per residue.  This compares
favorably with 2’-OMe-RNA at around 1.5° and RNA at 1.1° per residue.  In the meantime, base pair specificity remains intact.
2’-F-RNA phosphodiester linkages are not nuclease resistant, although the corresponding phosphorothioate linkages arehighly resistant.  Researchers usually design antisense oligonucleotides to form duplexes with RNA, which are then substrates
for RNase H.  Uniformly modified 2’-F-RNA/RNA duplexes are not substrates for RNase H.  However, it is straightforward
to prepare chimeric 2’-F-RNA/DNA phosphorothioate oligonucleotides which exhibit enhanced binding to the RNA target,
are substrates for RNase H, and are highly nuclease resistant.

Item

Catalog No.

Pack

2'-F-A-CE Phosphoramidite

10-3400-02
10-3400-05

0.25g
0.5g

2'-F-Ac-C-CE Phosphoramidite

10-3415-02
10-3415-05

0.25g
0.5g

2'-F-G-CE Phosphoramidite

10-3420-02
10-3420-05

0.25g
0.5g

2'-F-I-CE Phosphoramidite

NHBz
N

N

N

N
DMTO

NHAc

N

O
F
O P N(iPr)2
O CNEt2’-F-A

DMTO

O

O

N

F
O P N(iPr)2
O CNEt2’-F-Ac-C

10-3430-02
10-3430-05

0.25g
0.5g

10-3440-90
10-3440-02

100 µmole
0.25g

O

iBuHN
DMTO

O

DMTO

O

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)NOF
O P N(iPr)2F
O P N(iPr)22’-F-G

2’-F-UO CNEtAll minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

HN

N

N

OTHER INSTRUMENT TYPES

O

N

HN

Synthetic oligonucleotides
containing 2’-F-RNA linkages may
be deprotected with ammoniumhydroxide as normal.  Deprotection
using AMA at 65°C leads to somedegradation and so we recommend
the use of AMA at room
temperature for 2 hours.

RNA AND 2’-OMe-RNA

2'-F-U-CE Phosphoramidite

STABILITY NOTEO CNEt2’-F-I149

2’-F ANA SYNTHESIS
2’-F-ARABINONUCLEIC ACID (2’-F-ANA)
REFERENCES

Arabinonucleosides are epimers of ribonucleosides with the chiral switch being at the 2’ position of the sugar residue.   
2’-F-ANA adopts a more DNA-like B-type helix conformation, not through the typical C2’-endo conformation but, rather,through an unusual O4’-endo (east) pucker.  However, the presence of the electronegative fluorine leads to a still significant
increase (DTm1.2 °C/mod) in melting temperature per modification.1  2’-F-ANA-containing oligonucleotides exhibit very highbinding specificity to their targets.  Indeed, a single mismatch in a 2’-F-ANA – RNA duplex leads to a DTm of -7.2 °C and in a2’-F-ANA - DNA duplex a DTm of -3.9 °C.2

1. E. Viazovkina, M.M. Mangos, M.I.
Elzagheid, and M.J. Damha, Curr
Protoc Nucleic Acid Chem, 2002,
Chapter 4, Unit 4 15.
2. J.K. Watts, and M.J. Damha, Can. J.
Chem., 2008, 86, 641-656.
3. J.K. Watts, A. Katolik, J. Viladoms,
and M.J. Damha, Org Biomol Chem,
2009, 7, 1904-10.
4. A. Kalota, et al., Nucleic Acids Res.,
2006, 34, 451.
5. G.F. Deleavey, et al., Nucleic Acids
Res., 2010, 38, 4547-4557, J.K.
Watts, et al., Nucleic Acids Res.,
2007, 35, 1441-1451, T. Dowler,
et al., Nucleic Acids Res., 2006, 34,
1669-1675.

The presence of fluorine at the 2’ position in 2’-F-ANA leads to increased stability to hydrolysis under basic conditions relative
to RNA and even 2’-F-RNA.1,3  The stability of 2’-F-ANA to nucleases also makes this a useful modification for enhancing
the stability of oligonucleotides in biological environments.2  2’-F-ANA hybridizes strongly to target RNA and, unlike most
2’ modifications, induces cleavage of the target by RNase H.  Phosphorothioate (PS) 2’-F-ANA is routinely used in theseapplications due to its increased nuclease resistance.  Alternating 2’-F-ANA and DNA units provide among the highest
potency RNase H-activating oligomers.  Both the “altimer” and “gapmer” strand architectures consistently outperform
PS-DNA and DNA/RNA gapmers.4
siRNA oligos were found to tolerate the presence of 2’-F-ANA linkages very well.   High potency gene silencing wasdemonstrated5 with siRNA chimeras containing 2’-F-RNA and/or LNA and 2’-F-ANA.  The high efficacy of these chimeras was
attributed to the combination of the rigid RNA-like properties of 2’-F-RNA and LNA with the DNA-like properties of 2’-F-ANA.

INTELLECTUAL PROPERTY
2’-F-ANA is covered by intellectual
property.  Key patents covering siRNAand antisense applications are as
follows:
WO/2009/146556 (siRNA); WO
03064441 and WO 0220773(antisense).

Item

Catalog No.

Pack

2’-F-A-ANA CE Phosphoramidite

10-3800-90
10-3800-02

100 µmole
0.25g

STABILITY NOTE

2’-F-Bz-C-ANA CE Phosphoramidite

10-3810

Discontinued

Synthetic oligonucleotides
containing 2’-F-RNA linkages may
be deprotected with ammoniumhydroxide as normal.  Deprotection
using AMA at 65°C leads to somedegradation and so we recommend
the use of AMA at room
temperature for 2 hours.

2’-F-Ac-C-ANA CE Phosphoramidite

10-3815-02
10-3815-05

0.25g
0.5g

2’-F-G-ANA CE Phosphoramidite

10-3820-90
10-3820-02

100 µmole
0.25g

2’-F-U-ANA CE Phosphoramidite

10-3830-02
10-3830-05

0.25g
0.5g

2’-F-Me-U-ANA CE Phosphoramidite

10-3850-02
10-3850-05

0.25g
0.5g

NHBz
N

N

DMTO

O F
O

P

N(iPr)2O

CNEt

2'-F-A-ANA

150

NHAc

N

N

N

N

N

O

DMTO

O F
O

P

N(iPr)2

O

CNEt

N

O

DMTO

O F
O

P

N(iPr)2O

CNEt

2'-F-Ac-C-ANA

N

HN
iBuHN

O F
O

HN

N

N

DMTO

Chemical Formula: C41H49FN5O8P
Exact Mass: 789.33
Molecular Weight: 789.83
m/z: 789.33 (100.0%), 790.33 (46.5%), 791.34 (10.0%), 791.33 (2.5%), 792.34 (2.2%)
Elemental Analysis: C, 62.35; H, 6.25; F, 2.41; N, 8.87; O, 16.21; P, 3.92

2'-F-Bz-C-ANA

O

O

NHBz

P

N(iPr)2O

CNEt

2'-F-G-ANA

N

O
DMTO

O F

O

P

N(iPr)2O

CNEt

2'-F-U-ANA

2'-F-Me-U-ANA

2’-OME-RNA-PACE SYNTHESIS
2’-OME-RNA-PACE PHOSPHORAMIDITESAs an optimal cycle, we recommend using DCI as an activator (30-3150-XX) and a 15 minute coupling time.  Following
coupling, cap using Unicap (10-4410-XX) with a regular coupling time and then oxidize using 0.5 M CSO for 3 minutes.  
Alternatively, a 33 minute coupling time using 0.45 M tetrazole, oxidation using low-water iodine (40-4032-XX) followedby capping with 6.5% DMAP as Cap B will give acceptable results.  For deprotection, pre-treat the synthesis column with
1.5% DBU in anhydrous acetonitrile for 60 minutes at room temperature to remove 1,1-dimethyl-2-cyanoethyl protecting
groups. Rinse the column with acetonitrile, dry under argon and complete the deprotection with 40% aqueous methylamine
for 2 hours at room temperature.

Item

Catalog No.

Pack

2’-OMe-A-PACE Phosphoramidite

10-3150

Discontinued

2’-OMe-Ac-C-PACE Phosphoramidite

10-3151

Discontinued

2’-OMe-G-PACE Phosphoramidite

10-3152

Discontinued

2’-OMe-U-PACE Phosphoramidite

10-3153

Discontinued

REFERENCES
1. A. Hendel, et al., Nat Biotechnol, 2015,
33, 985-989.
2. D.E. Ryan, et al., Nucleic Acids Res,
2018, 46, 792-803.

INTELLECTUAL PROPERTY
These products are covered bypatent, US 7,067,641, and patents
pending owned by MetasenseTechnologies. Purchase of all or anyof these products includes a limited
license to use the products solely forthe manufacture of oligonucleotides
for research use only. This license
specifically excludes the use of
the product or oligonucleotides
containing the product for: (a)therapeutic or diagnostic applications(including kits, pools, libraries
and other products or services
that incorporate oligonucleotides
containing the product), (b) any invivo toxicity/safety study in supportof an investigational new drug
application (or foreign counterpart),or (c) resale (including sale of kits,
pools, libraries and other products orservices that incorporate the productor oligonucleotides containing the
product). If such activities havecommercial application, a separate
license is required from MetasenseTechnologies. Neither the product nor
any product created through its use
may be used in human clinical trials.
A simple agreement must be signed
before end-users and custom oligo
services may purchase these products
for use as defined above.  
https://www.glenresearch.com/media/
productattach/import/technical_note/
PACE.pdf

RELATED

NHBz
N

N

DMTO

DMTO

O

P

O

N(iPr)2
O

P

O
O

O

2’-OMe-A-PACE

2’-OMe-Ac-C-PACE

DMTO

O

OMe
O

N(iPr)2

CN

N

O

O

OMe

OMe
O

DMTO

O

HN

N

N

iBuHN

N

O

P

OMe

N(iPr)2O

CN

DNA PACE...................................41
DCI...............................................34
UniCap........................................36
0.5M CSO....................................36

O

N

HN

N

N

N

O

NHAc

O

P

N(iPr)2
O

CN

O

O

2’-OMe-G-PACE

2’-OMe-U-PACE

CN

151

RNA AND 2’-OMe-RNA

PACE modifications have enjoyed a resurgence in interest as applied to the field of CRISPR gene editing. In an
initial publication, it was shown that single guide RNAs (sgRNA) provided significantly higher activity in cells when2‘-O-methylthiophosphonoacetates were incorporated on the ends of the guide RNA to protect against cellular nucleases.1
In subsequent studies, 2’-OMe PACE modified sgRNAs were also shown to significantly increase on-target specificity of the
CRISPR-Cas9 DNA cleavage in eukaryotic cells. In a recent paper, the incorporation of 2’-OMe PACE modified nucleotides in
the 20-nucleotide guide region of the sgRNA was shown to decrease off-target cutting by over an order of magnitude while
in most cases increasing the overall on-target efficiency as compared to unmodified single guide RNA.2

NOTES

152

PURIFICATION
GLEN-PAK™ PURIFICATION
Glen-Pak™ DNA and RNA cartridges have advantages over Poly-Pak cartridges in that a single loading of the diluted crudedeprotection solution is all that is necessary.  Also, the range of purification has been extended to 100+ using DMT-ON oligos.
In addition, Glen-Pak cartridges allow purification of virtually the complete range of dyes and modifiers.  
The Glen-Pak DNA Cartridge 3g is a large cartridge capable of purifying 10-20 µmole oligonucleotide syntheses using thestandard DMT-ON procedure and Glen-Pak DNA 30mg 96-Well Plates are for parallel purification of up to 50 nmole scale
syntheses.  The Glen-Pak DNA 3mg 384-Well Plate is designed for use with 384-well plate compatible vacuum manifold
systems and can purify up to a 20 nmole scale synthesis.  Each well contains 3mg of Glen-Pak DNA resin, which binds about
15 nmoles of full length 40-mer DMT-ON oligo.
Scale suggestions for the Glen-Pak DNA product line are shown below:
Glen-Pak DNA ProductCatalog Number

Synthesis Scale Compatibility

60-5000-96
60-5100-XX and 60-5200-XX
60-5300-01
60-5400-01
60-5500-XX

10 nmole – 200 nmole
10 nmole – 1.0 µmole
5 µmole – 20 µmole
10 nmole – 50 nmole
Up to 20 nmole		Glen-Pak DNA 50mg Purification Cartridge
Glen-Pak DNA Purification Cartridge
Glen-Pak DNA Cartridge 3GGlen-Pak DNA 30mg 96-Well Plate
Glen-Pak DNA 3mg 384-Well Plate

A User Guide to Glen-Pak™ Purification describes in detail the process and several applications for DNA and RNA purification.  
This booklet is available online at:  https://www.glenresearch.com/media/productattach/g/l/glen-pak_2.9_1.pdf.

Catalog No.

Pack60-5000-96

Pack of 96

Glen-Pak™ DNA Purification Cartridge(For use in vacuum manifolds
and high-throughput devices)60-5100-10
60-5100-30
60-5100-96

Pack of 10
Pack of 30
Pack of 96

Glen-Pak™ DNA Purification Cartridge(For use with disposable syringes)

60-5200-01
60-5200-10

Pack of 1
Pack of 10

Glen-Pak™ DNA Cartridge 3g60-5300-01

Pack of 1

Glen-Pak™ DNA 30mg 96-Well Plate

60-5400-01

Pack of 1

Glen-Pak™ DNA 3mg 384-Well Plate

60-5500-01
60-5500-10

Pack of 1
Pack of 10

DNA Purification Cartridges
Glen-Pak™ 50mg DNA Purification Cartridge(For use in vacuum manifolds
and high-throughput devices)

Poly-Pak™ and Glen-Pak™ are trademarks of Glen Research Corporation

RELATED
Poly-Pak Reagents....................155

MISCELLANEOUS

Item

153

PURIFICATION
GLEN-PAK™ PURIFICATION (CONT.)
Item

Catalog No.

Pack

RNA Purification Cartridges
Glen-Pak™ RNA Purification Cartridge(For use in vacuum manifolds
and high-throughput devices)60-6100-10
60-6100-30
60-6100-96

Pack of 10
Pack of 30
Pack of 96

Glen-Pak™ RNA Purification Cartridge(For use with disposable syringes)

60-6200-01
60-6200-10

Pack of 1
Pack of 10

60-4120-82
60-4120-80

250mL
1L

60-0010-01

each

60-0020-01

each

Reagents
RNA Quenching Buffer
Racks and Seals
Adapter Rack
(For use with 96 well manifolds)
Seal for Adapter Rack
(For use on 96 well adapter rack)154

PURIFICATIONPOLY-PAK™ PURIFICATIONThe use of Poly-Pak™ packings in cartridges or barrels overcomes several disadvantages usually associated with reverse
phase (RP) cartridges.  The packing is stable in the pH range 1-13, thus the ammonium hydroxide solution, diluted withwater, is loaded directly onto the packing.  Also, after elution of failure sequences, the trityl group is removed and washedfrom the support-bound oligonucleotide.  The fully deprotected product can then be eluted and isolated by lyophilization.  
Poly-Pak™ Cartridges may also be used for desalting normal or labeled oligonucleotides.  The original Poly-Pak cartridge andbarrel are designed for 0.2 µmole syntheses or less.  Poly-Pak II cartridges and barrels are designed for use with 1 µmole
syntheses.  A booklet, User Guide To Poly-Pak™ Cartridge Purification, describes in detail the process and several applications.  
This booklet is available online at:  https://www.glenresearch.com/media/productattach/import/tbn/PolyPakBooklet.pdf

Item

Catalog No.

Pack

Poly-Pak™ Packing

60-1000-05
60-1000-25

5g
25g

Poly-Pak™ Cartridge

60-1100-01
60-1100-10

Pack of 1
Pack of 10

Poly-Pak™ II Cartridge

60-3100-01
60-3100-10

Pack of 1
Pack of 10

2.0M Triethylamine Acetate (TEAA)
HPLC Grade60-4110-52
60-4110-57
60-4110-60
60-4110-62

200mL
450mL
960mL
2L

2.0M Hexylammonium Acetate (HAA),
HPLC Grade, pH=7		
2% Aqueous Trifluoroacetic Acid

60-4210-52
60-4210-57

200mL
450mL

60-4040-57

450mL

Packing, Cartridges and Barrels

Poly-Pak Cartridge Used Manually

MISCELLANEOUS

Reagents

Poly-Pak™ is a trademark of Glen Research Corporation

155

PURIFICATIONGLEN GEL-PAK™ DESALTING
The principle of the Glen Research gel filtration column, Glen Gel-Pak™, is based on size exclusion chromatography that
separates molecules according to the hydrodynamic volume of the molecule in aqueous solutions.  In gel filtration, themobile phase for size exclusion is an aqueous solution and the stationary phase is a porous resin.  The pores of the resin
are sized such that they allow small molecules to enter the pores, yet exclude larger molecules from the pores.  The small
molecules, such as salts and hydrolyzed protecting groups, diffuse into the pores of the resin and move slowly throughthe column.  The larger molecules, such as DNA or proteins, are excluded from the pores and move quickly through thecolumn. The end result is that the larger molecules elute first in the column void volume while the small molecules are still
flowing through the resin of the column.
Glen Gel-Pak columns are ideal for desalting and reaction clean up.  They can be used for removal of the ammoniumhydroxide deprotection solution and hydrolyzed protecting groups after deprotection. The columns can also be used for theclean up of NHS-labeling reactions to separate the labeled oligo
and unlabeled oligo from the unreacted NHS ester, the hydrolyzed
label, and n-hydroxysuccinimide, thereby greatly simplifying thedownstream purification steps.
There are many benefits to Glen Gel-Pak columns:  
Versatility:• Ability to directly desalt oligonucleotides deprotected ineither 30% ammonium hydroxide OR 50:50 ammoniumhydroxide/40% aqueous methylamine (AMA)• Easily exchange buffers• Simple clean-up of labeling reactions• Mild method for purification from salts and solvents such as
DMSO and DMF
Capacity:

Glen Gel-Pak 0.2

Glen Gel-Pak 2.5

Glen Gel-Pak 1.0• Multiple column sizes (0.2 mL, 1.0 mL and 2.5 mL) are available to match synthesis scale• Ability to efficiently desalt short and long oligos at different scales using the same protocol• Suitable for oligos >10mer in length

156

Item

Catalog No.

Pack

Glen Gel-Pak™ 0.2 Desalting Column(0.2 mL Capacity)
Glen Gel-Pak™ 1.0 Desalting Column(1.0 mL Capacity)
Glen Gel-Pak™ 2.5 Desalting Column(2.5 mL Capacity)

61-5002-05
61-5002-50
61-5010-05
61-5010-50
61-5025-05
61-5025-25

Pack of 5
Pack of 50
Pack of 5
Pack of 50
Pack of 5
Pack of 25

Glen Gel-Pak™ is a trademark of Glen Research Corporation

PURIFICATIONOLIGO-AFFINITY SUPPORTWe expect that OAS PS will be used for purification of components from biological fluids.

Item

Catalog No.

Pack

Oligo-Affinity Support (PS)
(OAS PS)

26-4001-01
26-4001-02
26-4001-10

0.1g
0.25g
1.0g

26-4101-41

Pack of 4

Oligo-Affinity Support (PS)
1 µmole TWIST columns

OTHER INSTRUMENT TYPES
All minor bases, RNA products andmodifiers are packaged in septumcapped vials suitable for ABI and other
instruments.   If you would like anothertype of vial/column add the following to
the end of the catalog number.

Monomers
For Instrument type

Add

Expedite
MerMadeE
M

Columns
For Instrument type

Add

Expedite
Applied Biosystems 3900
MerMadeE
A
M(Please inquire for availability of vials andcolumns for other instrument types.)

O
PS

NH
N

N
DMTO

N

N
O

OAc OAc

OAS PSMISCELLANEOUS

Oligo-affinity supports (OAS) should ideally be compatible with automated synthesis, should be non-friable, should not shrinkor swell, and should have low non-specific binding of the proteins or DNA.  On the support shown below is an Adenosine
residue attached through the exocyclic amino group.  In this way, synthesis progresses regularly on removal of the 5’-DMT
group.  However, on treatment with ammonium hydroxide, the oligo is not cleaved from the support.  This matrix can thenbe used as an affinity support for a complementary segment of DNA or RNA.  Alternatively, the complementary strand can be
annealed to the support and the double stranded DNA can be used as an affinity support for purifying DNA binding proteins.

157

PHYSICAL DATAPHYSICAL DATA
The physical data table contains information which is unique to each monomer phosphoramidite.  The molecular weight(MW) is the formula weight of the fully-protected monomer phosphoramidite.  The MW is used to calculate the volume ofsolvent required to dilute 0.25g of the monomer to give a final 0.1M concentration.  This figure is also shown in the table.  
The unit molecular weight (Unit FW) is the formula weight of each monomer once inserted into an oligonucleotide withall protecting groups removed.  To obtain the molecular weight of a specific oligonucleotide, the following formula is used:
Oligonucleotide MW = Sum of Unit FW - 61.96

158

Cat. No.

Item

Phosphoramidite MW

10-0001
10-0101
10-0301
10-1000
10-1001
10-100310-1004
10-1006
10-100710-1008
10-1010
10-101410-1015
10-1016
10-1017
10-1018
10-1019
10-1020
10-102110-1027
10-1028
10-1029
10-1030
10-103110-1032
10-1034
10-1035
10-1036
10-1037
10-1038
10-1039
10-1040
10-1041
10-104210-1044
10-1046
10-1047
10-1048
10-1050
10-1051
10-1052
10-1053

dA-5’-CE Phosphoramidite
857.95dC-5’-CE Phosphoramidite
833.93dT-5’-CE Phosphoramidite
744.83dA-CE Phosphoramidite
857.957-Deaza-dA-CE Phosphoramidite
856.96N6-Me-dA-CE Phosphoramidite
767.863’-dA-CE Phosphoramidite
857.95Etheno-dA-CE Phosphoramidite
777.86
8-Br-dA-CE Phosphoramidite
887.818-oxo-dA-CE Phosphoramidite
873.95dC-CE Phosphoramidite
833.93
pdC-CE Phosphoramidite
907.1
Ac-dC-CE Phosphoramidite
771.85
TMP-F-dU-CE Phosphoramidite
866.97
Pyrrolo-dC-CE Phosphoramidite
767.85
5-Me-dC Brancher Phosphoramidite
942.1
Amino-Modifier C6 dC
1049.14
dG-CE Phosphoramidite
839.92
7-deaza-dG-CE Phosphoramidite
823.938-Br-dG-CE Phosphoramidite
903.98-oxo-dG-CE Phosphoramidite
855.93dmf-dG-CE Phosphoramidite
824.92dT-CE Phosphoramidite
744.835’-OMe-dT-CE Phosphoramidite
456.48
O4-Me-dT-CE Phosphoramidite
758.85
4-Thio-dT-CE Phosphoramidite
813.95
Carboxy-dT
814.882-Thio-dT-CE Phosphoramidite
879.02
Amino-Modifier C2 dT
938.94
Biotin-dT
1285.55
Amino-Modifier C6 dT
995.05dI-CE Phosphoramidite
754.792’-DeoxyNebularine-CE Phosphoramidite (Purine) 738.82
O6-Phenyl-dI-CE Phosphoramidite
830.925-Nitroindole-CE Phosphoramidite
780.862-Aminopurine-CE Phosphoramidite
809.01
dP-CE Phosphoramidite
771.85dK-CE Phosphoramidite
853.96
dU-CE Phosphoramidite
730.8
O4-Triazolyl-dU-CE Phosphoramidite
781.844-Thio-dU-CE Phosphoramidite
799.935-OH-dU-CE Phosphoramidite
788.83

Unit FW

Dilution (0.1M)

313.21
289.18304.2
313.21
312.22327.24313.21
337.23392.11
329.21
289.18327.23289.18307.18327.23402.36457.42329.21
328.22408.1
345.21
329.21304.2
318.22318.22320.26360.22320.26402.3
684.7
458.41
314.19298.19Varies340.23313.21330.23358.25290.17varies306.23306.170.25g/2.91mL
0.25g/3.00mL
0.25g/3.36mL
0.25g/2.91mL
0.25g/2.92mL
0.25g/3.26mL
0.25g/2.91mL
0.25g/3.21mL
0.25g/2.82mL
0.25g/2.86mL
0.25g/3.00mL
0.25g/2.76mL
0.25g/3.24mL
0.25g/2.88mL
0.25g/3.26mL
0.25g/2.65mL
0.25g/2.38mL
0.25g/2.98mL
0.25g/3.03mL
0.25g/2.77mL
0.25g/2.92mL
0.25g/3.03mL
0.25g/3.36mL
0.25g/5.48mL
0.25g/3.29mL
0.25g/3.07mL
0.25g/3.07mL
0.25g/2.84mL
0.25g/2.66mL
0.25g/1.94mL
0.25g/2.51mL
0.25g/3.31mL
0.25g/3.38mL
0.25g/3.01mL
0.25g/3.20mL
0.25g/3.09mL
0.25g/3.24mL
0.25g/2.93mL
0.25g/3.42mL
0.25g/3.20mL
0.25g/3.13mL
0.25g/3.17mL

PHYSICAL DATA
Item

Phosphoramidite MW

10-1054
10-1055
10-1056
10-1057
10-1058
10-1059
10-1060
10-1061
10-1062
10-1063
10-1064
10-1065
10-1066
10-1068
10-1070
10-1072
10-1073
10-1074
10-1076
10-1078
10-1079
10-1080
10-108110-1082
10-1083
10-1084
10-1085
10-1086
10-1088
10-1089
10-1090
10-1091
10-1092
10-109310-1096
10-1097
10-1098
10-1100
10-1115
10-1120
10-1130
10-1140
10-1150
10-1160
10-1170
10-1200
10-1210
10-1220
10-1230
10-1301
10-1315

pdU-CE Phosphoramidite
2’-deoxypseudoU-CE Phosphoramidite
Fluorescein-dT Phosphoramidite
TAMRA-dT
Dabcyl-dT
EDTA-C2-dT-CE Phosphoramidite
5-Me-dC-CE Phosphoramidite
5-Me-2’-deoxyZebularine-CE Phosphoramidite
5-Hydroxymethyl-dC-CE Phosphoramidite
5-OH-dC-CE Phosphoramidite
3’-dC-CE Phosphoramidite
dmf-5-Me-isodC-CE Phosphoramidite
5-Carboxy-dC-CE Phosphoramidite
N4-Et-dC-CE Phosphoramidite
O6-Me-dG-CE Phosphoramidite
6-thio-dG-CE Phosphoramidite
7-Deaza-8-aza-dG-CE Phosphoramidite (PPG)
3’-dG-CE Phosphoramidite
7-deaza-dX-CE Phosphoramidite
dmf-isodG-CE Phosphoramidite
8-Amino-dG-CE Phosphoramidite
5-Br-dC-CE Phosphoramidite
5-I-dC-CE Phosphoramidite
2-F-dI-CE Phosphoramidite
7-deaza-8-aza-dA-CE Phosphoramidite
3’-dT-CE Phosphoramidite
2-Amino-dA-CE Phosphoramidite
8-Amino-dA-CE Phosphoramidite
3-deaza-dA-CE Phosphoramidite
Amino-Modifier C6 dA
5-Br-dU-CE Phosphoramidite
5-I-dU-CE Phosphoramidite
5-F-dU-CE Phosphoramidite
5-Hydroxymethyl-dU-CE Phosphoramidite
Thymidine Glycol CE Phosphoramidite
AP-dC-CE Phosphoramidite
8,5’-Cyclo-dA CE Phosphoramidite
dA-Me Phosphonamidite
Ac-dC-Me Phosphonamidite
dG-Me Phosphonamidite
dT-Me Phosphonamidite
dA-PACE Phosphoramidite
Ac-dC-PACE Phosphoramidite
dG-PACE Phosphoramidite
dT-PACE Phosphoramidite
dA-H-Phosphonate, TEA Salt
dC-H-Phosphonate, DBU Salt
dG-H-Phosphonate, TEA Salt
dT-H-Phosphonate, TEA Salt
Pac-dA-Me Phosphoramidite
Ac-dC-Me Phosphoramidite

Unit FW

768.85328.22730.8
290.171425.57
815.711311.48870.851150.32709.7
1201.32676.53847.9
303.21728.82288.19917
319.21954.03305.18833.92289.18798.91
303.21905.97333.19757.87317.42853.97343.24934.97345.26824.91
329.2
824.92329.21769.83329.211020.13329.21895.01
344.22912.82368.08959.83415.08921.96varies, 2F=332.18
808.91313.2
744.83304.2
1047.33
328.22879.01
328.22856.95312.221068.14427.4
809.69369.07856.69416.07748.79308.16802.86320.191007.36338.21
974.97438.33855.92311.19802.91
311.24716.81
287.21784.89327.24689.79302.23928.02354.24841.93330.21910.01
370.24814.9
345.22822.9
313.21
849.35289.18804.88329.21709.78304.2
848.93 327.23 (Methyl triester)    
732.81 303.21 (Methyl triester)          Dilution (0.1M)
0.25g/3.25mL
0.25g/3.42mL
0.25g/1.75mL
0.25g/1.91mL
0.25g/2.17mL
0.25g/2.08mL
0.25g/2.95mL
0.25g/3.43mL
0.25g/2.73mL
0.25g/2.62mL
0.25g/3.00mL
0.25g/3.13mL
0.25g/2.76mL
0.25g/3.30mL
0.25g/2.93mL
0.25g/2.67mL
0.25g/3.03mL
0.25g/3.03mL
0.25g/3.25mL
0.25g/2.45mL
0.25g/2.79mL
0.25g/2.74mL
0.25g/2.60mL
0.25g/2.71mL
0.25g/3.09mL
0.25g/3.36mL
0.25g/2.39mL
0.25g/2.84mL
0.25g/2.92mL
0.25g/2.34mL
0.25g/3.09mL
0.25g/2.92mL
0.25g/3.34mL
0.25g/3.11mL
0.25g/2.48mL
0.25g/2.56mL
0.25g/2.92mL
0.25g/3.11mL
0.25g/3.49mL
0.25g/3.19mL
0.25g/3.62mL
0.25g/2.69mL
0.25g/2.97mL
0.25g/2.75mL
0.25g/3.07mL
0.25g/3.04mL
0.25g/2.94mL
0.25g/3.11mL
0.25g/3.52mL
0.25g/2.94mL
0.25g/3.41mL

MISCELLANEOUS

Cat. No.

159

PHYSICAL DATA

160

Cat. No.

Item

10-1321
10-1330
10-1440
10-1450
10-1460
10-1470
10-1501
10-1503
10-1504
10-1510
10-1511
10-1513
10-1514

iPr-Pac-dG-Me Phosphoramidite
dT-Me Phosphoramidite
CleanAmp™-Pac-dA-CE Phosphoramidite
CleanAmp™-Ac-dC-CE Phosphoramidite
CleanAmp™-Pac-dG-CE Phosphoramidite
CleanAmp™-dT-CE Phosphoramidite
1-Me-dA-CE Phosphoramidite
N6-Ac-N6-Me-dA-CE Phosphoramidite
def-dA-CE Phosphoramidite
5-Hydroxymethyl-dC II-CE Phosphoramidite
5-aza-5,6-dihydro-dC-CE Phosphoramidite
N4-Ac-N4-Et-dC-CE Phosphoramidite
5-Formyl-dC-CE Phosphoramidite

10-1516
10-1517
10-1518
10-1527
10-1529
10-1530
10-153110-1532
10-1533

tC-CE Phosphoramidite
tCO-CE Phosphoramidite
tCnitro-CE Phosphoramidite
dW-CE Phosphoramidite
N2-Amino-Modifier C6 dG
5,6-Dihydro-dT-CE Phosphoramidite
N3-Cyanoethyl-dT
5’-Dabsyl-dT-CE Phosphoramidite
DEACM Caged-dG-CE Phosphoramidite

10-1534
10-1535
10-1536
10-1537
10-1538
10-1539
10-1540
10-1541
10-1542
10-1543
10-1544
10-1545
10-1550
10-1554
10-1555
10-1560
10-1564

N-POM Caged-dT-CE Phosphoramidite
NHS-Carboxy-dT
Fmoc Amino-Modifier C6 dT
dX-CE Phosphoramidite
S-Bz-Thiol-Modifier C6-dT
DBCO-dT-CE Phosphoramidite
C8-Alkyne-dT-CE Phosphoramidite
C8-TIPS-Alkyne-dC-CE Phosphoramidite
C8-TMS-Alkyne-dC-CE Phosphoramidite
C8-Alkyne-dC-CE Phosphoramidite
C8-TIPS-Alkyne-dT-CE Phosphoramidite
C8-TMS-Alkyne-dT-CE Phosphoramidite
5,6-Dihydro-dU-CE Phosphoramidite
5-Ethynyl-dU-CE Phosphoramidite
TIPS-5-Ethynyl-dU-CE Phosphoramidite
Ac-5-Me-dC-CE Phosphoramidite
5-Formyl dC III CE Phosphoramidite

10-1576
10-1585
10-1590
10-1591
10-1598
10-1601
10-1621
10-1700
10-1710

Ferrocene-dT-CE Phosphoramidite
Pac-2-Amino-dA-CE Phosphoramidite
Pyrene-dU-CE Phosphoramidite
Perylene-dU-CE Phosphoramidite
8,5’-Cyclo-dG-CE Phosphoramidite
Pac-dA-CE Phosphoramidite
iPr-Pac-dG-CE Phosphoramidite
dA-Thiophosphoramidite
dC-Thiophosphoramidite

Phosphoramidite MW

Unit FW

907.01 343.23 (Methyl triester)    
705.79 318.22 (Methyl triester)
1045.25523.56 (triester)929.13499.54 (triester)
1061.25539.56 (triester)902.11514.55 (triester)
814.31
328.24809.89327.23836.97313.21785.82319.21787.89292.18799.89317.24915.96317.19 (formyl)
349.23 (diol)835.95395.33819.88379.26880.94440.32992.30311.23965.01428.38746.84306.21797.88357.26729.78591.531175.31558.49 (DEACM-dG)
329.21 (dG)
967.99527.38 (N-POM-dT)
897.91 varies, -CO2H=360.22
1121.28458.41(NH2)1069.1
330.191091.26546.531214.57
773.77834.94394.321094.4393.331010.24
393.33938.06393.33991.28394.32907.12394.32732.81
292.19754.81
314.19911.15314.19785.86303.21950.02317.19   
375.27 (acetal)
1125.07684.451042.21328.22955.04514.421005.1564.48619.65327.19887.97313.21946.05329.21955.09345.34 (dithioate)
931.07321.31 (dithioate)

Dilution (0.1M)
0.25g/2.76mL
0.25g/3.54mL
0.25g/2.39mL
0.25g/2.69mL
0.25g/2.36mL
0.25g/2.77mL
0.25g/3.07mL
0.25g/3.09mL
0.25g/2.99mL
0.25g/3.18mL
0.25g/3.17mL
0.25g/3.13mL
0.25g/2.73mL
0.25g/2.99mL
0.25g/3.05mL
0.25g/2.84mL
0.25g/2.52mL
0.25g/2.59mL
0.25g/3.35mL
0.25g/3.13mL
0.25g/3.43mL
0.25g/2.13mL
0.25g/2.58mL
0.25g/2.78mL
0.25g/2.23mL
0.25g/2.34mL
0.25g/2.29mL
0.25g/2.06mL
0.25g/2.99mL
0.25g/2.28mL
0.25g/2.47mL
0.25g/2.67mL
0.25g/2.52mL
0.25g/2.76mL
0.25g/3.41mL
0.25g/3.31mL
0.25g/2.74mL
0.25g/3.18mL
0.25g/2.63mL
0.25g/2.22mL
0.25g/2.40mL
0.25g/2.62mL
0.25g/2.49mL
0.25g/4.03mL
0.25g/2.82mL
0.25g/2.64mL
0.25g/1.75mL
0.25g /1.79mL

PHYSICAL DATA
Item

Phosphoramidite MW

10-1720
10-1730
10-1891
10-1900
10-1901
10-1902
10-1905
10-1906
10-1907
10-1908
10-1909
10-1910
10-1912
10-1913
10-1914
10-1915
10-1916
10-1917
10-1918
10-1919
10-1920
10-1922
10-1923
10-1925
10-1926
10-1927
10-1928
10-1931
10-1932
10-1933
10-1934
10-1935
10-1936

dG-Thiophosphoramidite
dT-Thiophosphoramidite
Methacrylate C6 Phosphoramidite
Chemical Phosphorylation Reagent
Chemical Phosphorylation Reagent II
Solid Chemical Phosphorylation Reagent II
5’-Amino-Modifier 55’-Amino-Modifier C65’-DMS(O)MT-Amino-Modifier C65’-Hexynyl Phosphoramidite
Spacer Phosphoramidite 9
1-Ethynyl-dSpacer CE Phosphoramidite
5’-Amino-Modifier C12
Spacer Phosphoramidite C3
dSpacer CE Phosphoramidite
Pyrrolidine-CE Phosphoramidite
5’-Amino-Modifier C6-TFA
5’-Amino-Modifier TEG CE-Phosphoramidite
Spacer Phosphoramidite 18
5’-Aminooxy-Modifier-11-CE Phosphoramidite
Symmetric Doubler Phosphoramidite
Trebler Phosphoramidite
5’-Amino-Modifier C3-TFA
Long Trebler Phosphoramidite
5’-Thiol-Modifier C6
Abasic II Phosphoramidite
Spacer C12 CE Phosphoramidite
5’-I-dT-CE Phosphoramidite
5’-Amino-dT-CE Phosphoramidite
5’-Aldehyde-Modifier C2 Phosphoramidite
5-Formylindole-CE Phosphoramidite
5’-Carboxy-Modifier C10
Thiol-Modifier C6 S-S

10-19385’-Maleimide-Modifier Phosphoramidite

10-1939
10-1941
10-1945
10-1946

Spermine Phosphoramidite
5’-DBCO-TEG Phosphoramidite
5’-Carboxy-Modifier C55’-Bromohexyl Phosphoramidite

10-1947
10-1948
10-1949
10-1952
10-1953
10-1954
10-1955
10-1963
10-1964

5’-Amino-Modifier C6-PDA
5’-Amino-Modifier C12-PDA
5’-Amino-Modifier TEG PDA
DesthiobiotinTEG Phosphoramidite
Biotin Phosphoramidite
5'-Biotin II Phosphoramidite
BiotinTEG Phosphoramidite
Fluorescein Phosphoramidite
6-Fluorescein Phosphoramidite

Unit FW

Dilution (0.1M)

937.07361.34 (dithioate)
841.97336.32 (dithioate)
385.48247.23656.7779.98
722.82
79.98
692.7979.98
577.71
167.1
589.76179.16681.34179.16298.36160.11652.77212.14644.74204.12673.92263.32578.69138.06620.73180.1
841.97178.1
413.42
179.16489.47255.21
784.93344.3
711.82271.211095.32
351.311417.72370.33371.34137.081475.78428.41576.78196.2
750.98196.1
704.93264.3
552.35414.09713.81
303.21480.58228.14763.86323.24
485.56 varies, -CO2H = 250.23
769.05328.4 (disulfide)
196.2 (thiol)
437.47 299.22 (pre-retro-DA)   
203.09 (maleimide)
1233.17408.52708.82570.57595.11
180.1
381.29243.04 (bromide)
205.15 (azide)478.57179.15562.7
263.32554.62
255.21
980.19539.56876.1
435.48834.03393.391010.24569.611207.5598.561176.35
566.480.25g/1.78mL
0.25g/1.98mL
0.25g/6.49mL
0.25g/3.81mL
0.25g/3.46mL
0.25g/3.61mL
0.25g/4.33mL
0.25g/4.24mL
0.25g/3.67mL
0.25g/8.38mL
0.25g/3.83mL
0.25g/3.88mL
0.25g/3.71mL
0.25g/4.32mL
0.25g/4.03mL
0.25g/2.97mL
0.25g/6.05mL
0.25g/5.11mL
0.25g/3.18mL
0.25g/3.51mL
0.25g/2.28mL
0.25g/1.76mL
0.25g/6.73mL
0.25g/1.69mL
0.25g/4.33mL
0.25g/3.33mL
0.25g/3.55mL
0.25g/4.53mL
0.25g/3.50mL
0.25g/5.20mL
0.25g/3.27mL
0.25g/5.15mL
0.25g/3.25mL
0.25g/5.71mL
0.25g/2.03mL
0.25g/3.53mL
0.25g/4.20mL
0.25g/6.56mL

MISCELLANEOUS

Cat. No.

0.25g/5.22mL
0.25g/4.44mL
0.25g/4.51mL
0.25g/2.55mL
0.25g/2.85mL
0.25g/3.00mL
0.25g/2.47mL
0.25g/2.07mL
0.25g/2.13mL

161

PHYSICAL DATA

162

Cat. No.

Item

Phosphoramidite MW

10-1973
10-1974
10-1975
10-1976
10-1977
10-1978
10-1979
10-1981
10-1982
10-1983
10-1985
10-1986
10-1987
10-1991
10-1992
10-1993
10-1994
10-1995
10-1996
10-1997
10-1998
10-2000
10-2011
10-2029
10-2030
10-3000
10-2101
10-2115
10-2121
10-2130
10-300310-3004
10-3005
10-301110-301210-301410-3015
10-301710-302110-3024
10-3025
10-3030
10-3034
10-3039
10-3040
10-3050
10-3052
10-3055
10-3056
10-3064
10-3070

Acridine Phosphoramidite
5’-GalNAc C3 Phosphoramidite
Cholesteryl-TEG Phosphoramidite
5’-Cholesteryl-TEG Phosphoramidite
a-Tocopherol-TEG Phosphoramidite
Palmitate Phosphoramidite
Stearyl Phosphoramidite
Asymmetric Doubler (Lev) Phosphoramidite
Psoralen C2 Phosphoramidite
Psoralen C6 Phosphoramidite
DNP-TEG Phosphoramidite
5’-Trimethoxystilbene Cap Phosphoramidite
5’-Pyrene Cap Phosphoramidite
Dithiol Serinol Phosphoramidite
Alkyne-Modifier Serinol Phosphoramidite
Protected Biotin Serinol Phosphoramidite
6-Fluorescein Serinol Phosphoramidite
Protected BiotinLC Serinol Phosphoramidite
COT Serinol Phosphoramidite
Amino-Modifier Serinol Phosphoramidite
DBCO-Serinol Phosphoramidite
Bz-A-LA-CE Phosphoramidite
5-Me-Bz-C-LA-CE Phosphoramidite
dmf-G-LA-CE Phosphoramidite
T-LA-CE Phosphoramidite
Pac-A-CE Phosphoramidite
beta-L-Pac-dA-CE Phosphoramidite
beta-L-Ac-dC-CE Phosphoramidite
beta-L-iPr-dG-CE Phosphoramidite
beta-L-dT-CE Phosphoramidite
Bz-A-CE Phosphoramidite
A-TOM-CE Phosphoramidite
N6-Methyl-A-CE Phosphoramidite
Zebularine-CE Phosphoramidite
Pyridin-2-one-CE Phosphoramidite
C-TOM-CE Phosphoramidite
Ac-C-CE Phosphoramidite
Pyrrolo-C-TOM-CE Phosphoramidite
iPr-Pac-G-CE Phosphoramidite
G-TOM-CE Phosphoramidite
Ac-G-CE Phosphoramidite
U-CE Phosphoramidite
U-TOM-CE Phosphoramidite
Amino-Modifier C6-U Phosphoramidite
I-CE Phosphoramidite
5-Me-U-CE Phosphoramidite
4-Thio-U-TOM-CE Phosphoramidite
PseudoUridine-CE Phosphoramidite
1-Methyl-PseudoUridine Phosphoramidite
5-Me-C-TOM-CE Phosphoramidite
2-Aminopurine-TBDMS-CE Phosphoramidite

891.531206.38
1196.6820.131139.56555.83470.71891.04502.55558.65950.00571.65501.6853.08758.881051.28
1191.31298.57
822.97887.01909.08885.96875.96852.93772.84
1018.23887.97771.85946.05744.83988.21998.241032.25845.05844.06974.22902.11970.231076.311014.24
941.43861.06933.171197.41885.08875.081002.29861.05875.07988.25954.19Unit FW

Dilution (0.1M)

450.86609.61755.97682.89698.91417.57332.46352.32364.29420.4
509.41433.39363.35412.46318.26450.45582.45697.74382.35224.15468.45341.22331.22357.22332.20329.21
313.21
289.18329.21304.20329.21
329.21
343.23290.17289.18305.18305.18343.27345.21345.21345.21306.17306.17474.4
330.19320.19322.22306.17320.19319.21
329.210.25g/2.80mL
0.25g/2.07mL
0.25g/2.09mL
0.25g/3.05mL
0.25g/2.19mL
0.25g/4.50mL
0.25g/5.31mL
0.25g/2.81mL
0.25g/4.97mL
0.25g/4.48mL
0.25g/2.63mL
0.25g/4.37mL
0.25g/4.98mL
0.25g/2.93mL
0.25g/3.29mL
0.25g/2.38mL
0.25g/2.10mL
0.25g/1.93mL
0.25g/3.04mL
0.25g/2.82mL
0.25g/2.75mL
0.25g/2.82mL
0.25g/2.85mL
0.25g/2.93mL
0.25g/3.23mL
0.25g/2.46mL
0.25g/2.82mL
0.25g/3.24mL
0.25g/2.64mL
0.25g/3.36mL
0.25g/2.53mL
0.25g/2.50mL
0.25g/2.42mL
0.25g/2.96mL
0.25g/2.96mL
0.25g/2.57mL
0.25g/2.77mL
0.25g/2.58mL
0.25g/2.32mL
0.25g/2.46mL
0.25g/2.66mL
0.25g/2.90mL
0.25g/2.68mL
0.25g/2.09mL
0.25g/2.82mL
0.25g/2.86mL
0.25g/2.49mL
0.25g/2.90mL
0.25g/2.86mL
0.25g/2.53mL
0.25g/2.62mL

Cat. No.

Item

Phosphoramidite MW

10-3072
10-3083
10-3085
10-3090
10-3091
10-3100
10-311010-311110-3115
10-3116
10-3120
10-312110-3123
10-3124
10-3130
10-3131
10-3132
10-3140
10-3150
10-3151
10-3152
10-3153
10-3160
10-3170
10-3171
10-3172
10-3173
10-319010-3200
10-321110-3220
10-3231
10-3400
10-3415
10-3420
10-3430
10-3440
10-3501
10-3517
10-3601
10-3621
10-3800
10-3815
10-3820
10-3830
10-3850
10-3914
10-3915
10-4191
10-441010-4906

6-Thio-G-CE Phosphoramidite
1039.31
8-Aza-7-deaza-A-CE Phosphoramidite
939.162,6-Diaminopurine-TOM-CE Phosphoramidite
1113.36
Br-U-CE Phosphoramidite
939.96
5-I-U-CE Phosphoramidite
986.962’-OMe-A-CE Phosphoramidite
887.972’-OMe-C-CE Phosphoramidite
863.952’-OMe-TMP-5-F-U-CE Phosphoramidite
897.082’-OMe-Ac-C-CE Phosphoramidite
801.882’-OMe-3-deaza-5-aza-C-CE Phosphoramidite
816.912’-OMe-ibu-G-CE Phosphoramidite
869.972’-OMe-G-CE Phosphoramidite
854.932’-OMe-2-Aminopurine-CE Phosphoramidite
839.042’-OMe-2,6-Diaminopurine-CE Phosphoramidite 924.05
2’-OMe-U-CE Phosphoramidite
760.822’-OMe-5-Me-U-CE Phosphoramidite
774.842’-OMe-5-F-U-CE Phosphoramidite
778.782’-OMe-I-CE Phosphoramidite
784.852’-OMe-A-PACE Phosphoramidite
958.072’-OMe-Ac-C-PACE Phosphoramidite
871.972’-OMe-G-PACE Phosphoramidite
940.052’-OMe-U-PACE Phosphoramidite
830.922’-OMe-5-Me-C-CE Phosphoramidite
815.9
2’-OMe-A-Thiophosphoramidite
985.122’-OMe-C-Thiophosphoramidite
899.022’-OMe-G-Thiophosphoramidite
967.1
2’-OMe-U-Thiophosphoramidite
857.972’-OMe-5-Br-U-CE Phosphoramidite
839.72A-2'-MOE-Phosphoramidite
932.035-Me-C-2'-MOE-Phosphoramidite
922.03G-2'-MOE-Phosphoramidite
914.01
5-Me-U-2'-MOE-Phosphoramidite
818.902’-F-A-CE Phosphoramidite
875.932’-F-Ac-C-CE Phosphoramidite
789.842’-F-G-CE Phosphoramidite
857.912’-F-U-CE Phosphoramidite
748.792’-F-I-CE Phosphoramidite
772.82
1-Me-A-CE Phosphoramidite
944.57
Ribo-tC° Phosphoramidite
950.162’-OMe-Pac-A-CE Phosphoramidite
917.992’-OMe-iPr-Pac-G-CE Phosphoramidite
976.072’-FANA-A-CE Phosphoramidite
875.932’-FANA-Ac-C-CE Phosphoramidite
789.832’-FANA-G-CE Phosphoramidite
857.912’-FANA-U-CE Phosphoramidite
748.792’-F-5-Me-U-ANA-CE Phosphoramidite
762.80rSpacer CE Phosphoramidite
823.09rSpacer TBDMS CE Phosphoramidite
750.99dSpacer-5’-CE Phosphoramidite
620.73
UniCap Phosphoramidite
334.39PC Amino-Modifier Phosphoramidite
605.59Unit FW

Dilution (0.1M)

361.26329.21
344.22385.06432.07343.24319.21
337.2
319.21
319.21359.24359.24343.24358.25320.2
334.22338.19344.22385.27361.25401.27362.23333.24375.36351.34391.36352.32399.09387.29377.29403.29378.27331.2
307.18347.19308.16332.18344.24395.26343.24359.24331.2
307.17347.19308.16322.18196.09196.09180.100.25g/2.41mL
0.25g/2.66mL
0.25g/2.25mL
0.25g/2.66mL
0.25g/2.53mL
0.25g/2.82mL
0.25g/2.89mL
0.25g/2.79mL
0.25g/3.12mL
0.25g/3.06mL
0.25g/2.87mL
0.25g/2.92mL
0.25g/2.98mL
0.25g/2.71mL
0.25g/3.29mL
0.25g/3.23mL
0.25g/3.21mL
0.25g/3.19mL
0.25g/2.61mL
0.25g/2.87mL
0.25g/2.66mL
0.25g/3.01mL
0.25g/3.06mL
0.25g/1.69mL
0.25g/1.85mL
0.25g/1.72mL
0.25g/1.94mL
0.25g/2.98mL
0.25g/2.68mL
0.25g/2.71mL
0.25g/2.74mL
0.25g/3.05mL
0.25g/2.85mL
0.25g/3.17mL
0.25g/2.91mL
0.25g/3.34mL
0.25g/3.23mL
0.25g/2.65mL
0.25g/2.63mL
0.25g/2.72mL
0.25g/2.56mL
0.25g/2.85mL
0.25g/3.16mL
0.25g/2.91mL
0.25g/3.34mL
0.25g/3.28mL
0.25g/3.04mL
0.25g/3.33mL
0.25g/4.03mL
0.25g/7.48mL
0.25g/4.13mL

371.32MISCELLANEOUS

PHYSICAL DATA

163

PHYSICAL DATA
Cat. No.

Item

10-4913
10-4920
10-4950
10-4960
10-5000
10-5101
10-5800
10-5901
10-5902
10-5903
10-5905
10-5906

PC Spacer Phosphoramidite
PC Linker Phosphoramidite
PC Biotin Phosphoramidite
3-Cyanovinylcarbazole Phosphoramidite (CNVK)
Universal-CE Phosphoramidite
Ac-dC-5'-CE Phosphoramidite
Azobenzene Phosphoramidite
5’-Fluorescein Phosphoramidite
5’-Hexachloro-Fluorescein Phosphoramidite
5’-Tetrachloro-Fluorescein Phosphoramidite
SIMA (HEX) Phosphoramidite
5’-Dichloro-dimethoxy-Fluorescein
Phosphoramidite II
5’-Dabcyl Phosphoramidite
Cyanine 3 Phosphoramidite
JOE-dT Phosphoramidite
Quasar® 570-dT Phosphoramidite
Quasar® 670-dT Phosphoramidite
Cyanine 3.5 Phosphoramidite
Cyanine 5 Phosphoramidite
Cyanine 5.5 Phosphoramidite
Redmond Red® Phosphoramidite
Yakima Yellow® Phosphoramidite
5’-AquaPhluor® 593 CE Phosphoramidite
5’-CDPI3 MGB™ Phosphoramidite
Eclipse® Quencher Phosphoramidite
5’-BHQ-1 Phosphoramidite
5’-BHQ-2 Phosphoramidite
5’-BBQ-650®-CE Phosphoramidite
BHQ-1-dT
BHQ-2-dT
BBQ-650®-dT-CE Phosphoramidite
SIMA (HEX)-dT Phosphoramidite
5’-Biotin Phosphoramidite
Methylene Blue II Phosphoramidite
2’,3’-ddA-CE Phosphoramidite
2’,3’-ddC-CE Phosphoramidite
2’,3’-ddG-CE Phosphoramidite
2’,3’-ddT-CE Phosphoramidite
dmf-dG-5’-CE Phosphoramidite
Cis-syn Thymine Dimer Phosphoramidite
AAA Trimer Phosphoramidite
AAC Trimer Phosphoramidite
ACC Trimer Phosphoramidite
ACT Trimer Phosphoramidite
AGA Trimer Phosphoramidite
ATC Trimer Phosphoramidite
ATG Trimer Phosphoramidite
CAG Trimer Phosphoramidite
CAT Trimer Phosphoramidite
CCA Trimer Phosphoramidite

10-591210-5913
10-5936
10-5953
10-5955
10-5914
10-5915
10-5916
10-5920
10-5921
10-5923
10-5924
10-5925
10-593110-5932
10-5934
10-5941
10-5942
10-5944
10-5945
10-5950
10-5961
10-7001
10-7101
10-7201
10-7301
10-9201
11-1330
13-1000
13-1001
13-1011
13-1013
13-1020
13-103113-1032
13-1102
13-1103
13-1110164

Phosphoramidite MW
784.88699.781038.25836.95801.87771.85815.94843.951050.62981.731065.02972.88568.69953.641552.51497.651523.69
1053.76
979.681171.25971.091023.811239.171323.42978.5
676.75678.72802.9
1401.561403.53
1441.57
1646.64846.08967.67574.7
550.68506.54426.45824.921024.01
1911.5
1887.5
1863.51774.5
1893.51774.51780.51869.51774.5
1863.5

Unit FW

Dilution (0.1M)

344.26259.15597.62396.330.25g/3.19mL
0.25g/3.57mL
0.25g/2.41mL
0.25g/2.99mL
0.25g/3.12mL
0.25g/3.24mL
0.25g/3.06mL
0.25g/2.96mL
0.25g/2.38mL
0.25g/2.55mL
0.25g/2.35mL
0.25g/2.57mL

289.18375.32537.46744.13675.24759.54666.4
430.18507.59944.2
911.05937.09607.7
533.63633.74445.34718.33787.82872.96537.89538.49540.47665.65960.93962.911000.95
1037.79405.45489.57297.21
273.18313.2
288.19329.21
608.390.25g/4.40mL
0.25g/2.62mL
0.25g/1.61mL
0.25g/1.67mL
0.25g/1.64mL
0.25g/2.37mL
0.25g/2.55mL
0.25g/2.13mL
0.25g/2.57mL
0.25g/2.44mL
0.25g/2.02mL
0.25g/1.89mL
0.25g/2.55mL
0.25g/3.69mL
0.25g/3.68mL
0.25g/3.11mL
0.25g/1.78mL
0.25g/1.78mL
0.25g/1.73mL
0.25g/1.52mL
0.25g/2.95mL
0.25g/2.58mL
0.25g/4.35mL
0.25g/4.54mL
0.25g/4.94mL
0.25g/5.86mL
0.25g/3.03mL
0.25g/2.44mL
0.25g/1.31mL
0.25g/1.32mL
0.25g/1.34mL
0.25g/1.41mL
0.25g/1.32mL
0.25g/1.41mL
0.25g/1.40mL
0.25g/1.34mL
0.25g/1.41mL
0.25g/1.34mL

PHYSICAL DATA
Item

13-1112
13-1122
13-1123
13-1132
13-1200
13-1201
13-120313-121013-121213-1213
13-1223
13-1230
13-1233
13-1301
13-1313
13-132113-132213-133113-1333
20-0002
20-0102
20-0202
20-0302
20-2000
20-2001
20-2002
20-2004
20-201020-201120-201220-2013
20-2015
20-2017
20-2019
20-2020
20-2021
20-2022
20-2029
20-2030
20-2031
20-2032
20-2040
20-2041
20-2050
20-2051
20-2056
20-2064
20-2074
20-2084
20-2090
20-2101-61

CCG Trimer Phosphoramidite
CGG Trimer Phosphoramidite
CGT Trimer Phosphoramidite
CTG Trimer Phosphoramidite
GAA Trimer Phosphoramidite
GAC Trimer Phosphoramidite
GAT Trimer Phosphoramidite
GCA Trimer Phosphoramidite
GCG Trimer Phosphoramidite
GCT Trimer Phosphoramidite
GGT Trimer Phosphoramidite
GTA Trimer Phosphoramidite
GTT Trimer Phosphoramidite
TAC Trimer Phosphoramidite
TCT Trimer Phosphoramidite
TGC Trimer Phosphoramidite
TGG Trimer Phosphoramidite
TTC Trimer Phosphoramidite
TTT Trimer Phosphoramidite
dA-5’-CPG
dC-5’-CPG
dG-5’-CPG
dT-5’-CPG
dA-CPG 500
dA-CPG 1000
dA-CPG 2000
3’-dA-CPG
dC-CPG 500
dC-CPG 1000
dC-CPG 2000
Ac-dC-CPG 500
Ac-dC-CPG 1000
2’,3’-ddC-CPG
3’-Amino-Modifier C6 dC CPG
dG-CPG 500
dG-CPG 1000
dG-CPG 2000
dmf-dG-CPG
dT-CPG 500
dT-CPG 1000
dT-CPG 2000
dI-CPG 500
dI-CPG 1000
dU-CPG 500
dU-CPG 1000
3’-Fluorescein-dT CPG
3’-dC-CPG
3’-dG-CPG
3’-dT-CPG
5-Br-dU-CPG
dA-CPG 1000

Phosphoramidite MW

Unit FW

1845.51851.51756.51756.5
1893.51869.51780.51869.51851.51756.51762.51780.51667.51774.5
1661.41756.51762.5
1661.41572.4

Dilution (0.1M)
0.25g/1.35mL
0.25g/1.35mL
0.25g/1.42mL
0.25g/1.42mL
0.25g/1.32mL
0.25g/1.34mL
0.25g/1.40mL
0.25g/1.34mL
0.25g/1.35mL
0.25g/1.42mL
0.25g/1.42mL
0.25g/1.40mL
0.25g/1.50mL
0.25g/1.41mL
0.25g/1.50mL
0.25g/1.42mL
0.25g/1.42mL
0.25g/1.50mL
0.25g/1.59mL

313.21
289.18329.21304.2
313.21
313.21
313.21
313.21
289.18289.18289.18289.18289.18273.19457.42329.21
329.21
329.21
329.21
304.2
304.2
304.2
314.19314.19290.17290.17815.71
289.18329.21304.2
369.07313.21MISCELLANEOUS

Cat. No.

165

PHYSICAL DATA

166

Cat. No.

Item

20-2101-62
20-2101-65
20-2115-61
20-2115-62
20-2115-65
20-2129-61
20-2129-62
20-2129-65
20-2131-61
20-2131-62
20-2131-65
20-2501
20-251120-2529
20-2530
20-2601
20-262120-2900
20-2902
20-2903
20-2913
20-2933
20-2938
20-2952
20-2954
20-2955
20-2956
20-2958
20-2961
20-2963
20-2964
20-2973
20-2974
20-2975
20-2980
20-2981
20-2982
20-2991
20-2992
20-2993
20-2994
20-2995
20-2997
20-2999
20-3300
20-3303
20-3304
20-3315
20-332120-3324
20-3330

dA-CPG 1000
dA-CPG 1000
Ac-dC-CPG 1000
Ac-dC-CPG 1000
Ac-dC-CPG 1000
dmf-dG-CPG
dmf-dG-CPG
dmf-dG-CPG
dT-CPG 1000
dT-CPG 1000
dT-CPG 1000
Bz-A-LA-CPG
Bz-5-Me-C-LA-CPG
dmf-G-LA-CPG
T-LA-CPG
Pac-dA-CPG
iPr-Pac-dG-CPG
3’-Phosphate CPG
3’-Glyceryl CPG
3’-CPR II CPG
3’-Spacer C3 CPG
3’-Thiol-Modifier C3 S-S CPG
3’-Thiol-Modifier 6 S-S CPG
DesthiobiotinTEG-CPG
3’-PT-Amino-Modifier C3 CPG
3’-BiotinTEG CPG
3’-PT-Amino-Modifier C6 CPG
3’-Amino-Modifier C7 CPG 1000
3’-(6-FAM) CPG
3’-Fluorescein CPG
3’-(6-Fluorescein) CPG
3’-Acridine CPG
GalNAc C3 CPG
3’-Cholesteryl-TEG CPG
3’-Uaq Cap CPG
3’-Amino-dT CPG
3’-Propargyl-5-Me-dC CPG
3’-Dithiol Serinol CPG
3’-Alkyne-Modifier Serinol CPG
3’-Protected Biotin Serinol CPG
3’-6-Fluorescein Serinol CPG
3’-Protected BiotinLC Serinol CPG
3’-Amino-Modifier Serinol CPG
3'-Azido-Modifier Serinol CPG
Pac-A-RNA-CPG
Bz-A-RNA-CPG
Ac-A-RNA-CPG
Ac-C-RNA-CPG
iPr-Pac-G-RNA-CPG
Ac-G-RNA-CPG
U-RNA-CPG

Phosphoramidite MW

Unit FW

313.21
313.21
289.18289.18289.18329.21
329.21
329.21
304.2
304.2
304.2
341.22331.22357.22332.2
313.21
329.21
79.98
154.0679.98
138.06154.12 (thiol), 244.27 (disulfide)
198.18 (thiol), 332.37 (disulfide)
539.56137.07569.61
179.15209.18569.46598.56566.48450.86609.61755.97539.39303.21
341.26412.46334.26450.45584.47697.74224.15335.26329.21
329.21
329.21305.18345.21345.21306.17

Dilution (0.1M)

PHYSICAL DATA
Item

20-3600
2’-OMe-A-RNA-CPG
20-36102’-OMe-C-RNA-CPG
20-3615
2’-OMe-Ac-C-RNA-CPG
20-3621
2’-OMe-G-RNA-CPG
20-3630
2’-OMe-U-RNA-CPG
20-4040
Puromycin-CPG
20-59103’-TAMRA CPG
20-59113’-Dabsyl CPG
20-59123’-Dabcyl CPG
20-5913
Cyanine 3 CPG
20-5915
Cyanine 5 CPG
Redmond Red® CPG
20-5921
Yakima Yellow® CPG
20-5923
AquaPhluor® 593 CPG
20-5924
CDPI3 MGB™ CPG
20-5925
Eclipse® Quencher CPG
20-5927
MGB Eclipse® CPG
20-59313’-BHQ-1 CPG
20-5932
3’-BHQ-2 CPG
20-5933
3’-BHQ-3 CPG
20-5934
BBQ-650® CPG
20-9202
dmf-dG-5’-CPG
21-2000
dA-Q-CPG 500
21-2010dC-Q-CPG 500
21-2013
Ac-dC-Q-CPG 500
21-2029
dmf-dG-Q-CPG  50021-2030
dT-Q-CPG 500
25-2000
dA-High Load-CPG
25-2010dC-High Load-CPG
25-2020
dG-High Load CPG
25-2030
dT-High Load-CPG
25-2900
3’-Phosphate CPG (High Load)
26-2600
dA PS
26-2610dC PS
26-2629
dmf-dG PS
26-2630
dT-PS
26-2900
3’-Phosphate PS
26-2955
3’-BiotinTEG PS
26-2956
3’-PT-Amino-Modifier C6 PS
26-29613’-(6-FAM) PS
26-59103’-TAMRA PS
26-59123’-Dabcyl PS
50-1904
Azidobutyrate NHS Ester
50-1905
Alkyne-NHS Ester
50-1938
Maleimide NHS Ester (SMCC)
50-1941
DBCO-sulfo-NHS Ester
50-1960
Methylene Blue NHS Ester
50-1970
Thiazole Orange NHS Ester
50-2000
BiotinTEG Azide
50-2001
DesthiobiotinTEG Azide
50-2002
Dipivaloyl 6-FAM-TEG Azide

MW

226.19225.2
334.32532.5
538.96538.06444.55414.5
744.79Unit FW
343.24319.21
319.21359.24320.2
533.48623.6
498.49462.44507.59533.63445.34718.33900.93831.87537.891120.56554.49556.47597.63667.63329.21
313.21
289.18305.18329.21304.2
313.21
289.18329.21
304.2
79.98
313.21
289.18329.21
304.2
79.98
569.61
179.15569.46623.6
462.44113.12110.11
219.23316.37425.89386.51

Dilution (0.1M)

20-5920MISCELLANEOUS

Cat. No.

167

PHYSICAL DATA

168

Cat. No.

Item

50-200350-2004
50-2005
50-200650-200750-2008
50-200950-201050-590150-591050-591150-591350-4950

6-FAM-TEG Azide
Coumarin Azide
6-HEX Azide
6-TET Azide
TEMPO Azide
TEMPO-TEG Azide
Psoralen Azide
Disulfo-Cyanine 7 Azide
Fluorescein NHS ester
TAMRA NHS Ester
ROX NHS Ester
sulfoCyanine 3 NHS Ester
PC Biotin NHS Ester

Phosphoramidite MW

Unit FW

576.55203.15665.09596.2
197.26373.47283.28829.08473.39527.53631.69751.91840.90358.31
413.45516.60598.73725.81

Dilution (0.1M)

INDEX
Symbols2'-5' Linkages

3’-dA-CE Phosphoramidite  71
3’-dA-CPG  71
3’-dC-CE Phosphoramidite  71
3’-dC-CPG  71
3’-dG-CE Phosphoramidite  71
3’-dG-CPG  72
3’-dT-CE Phosphoramidite  71
3’-dT-CPG  72

2’-5’ Linked Oligonucleotides 70, 72
5’ -> 3’ SYNTHESIS
5’-CE Phosphoramidites  38

5’-AquaPhluor® 639 Phosphoramidite 114

AA

1-Me-A-CE Phosphoramidite  1411-Me-dA-CE Phosphoramidite  72
2’,3’-ddA  62
2’-F-A-ANA CE Phosphoramidite  1502'-F-A-CE Phosphoramidite  1492'-OMe-A-CE Phosphoramidite  1432’-OMe-A-PACE Phosphoramidite  1512'-OMe-A-RNA  1452'-OMe-Pac-A-CE Phosphoramidite  1443'-dA-CE Phosphoramidite  71
3'-dA-CPG  61, 72
7-Deaza-dA-CE Phosphoramidite  63
8-Amino-dA-CE Phosphoramidite  65
8-Br-dA-CE Phosphoramidite  66
8-Oxo-dA-CE Phosphoramidite  67
A-2'-MOE-Phosphoramidite  148Ac-A-RNA-CPG  132Amino-Modifier C6 dA  83
A-TOM-CE Phosphoramidite  132Bz-A-CE Phosphoramidite  134Bz-A-LNA-CE Phosphoramidite  44
Bz-A-RNA-CPG  131, 135
dA-CE Phosphoramidite  8, 12, 15, 16, 18, 20, 22
dA-H-Phosphonate  43
dA-Me Phosphonamidite  40
dA-Me Phosphoramidite  42
dA-PACE Phosphoramidite  41
dA-Thiophosphoramidite  147def-dA-CE Phosphoramidite  26
N6-Ac-N6-Me-dA-CE Phosphoramidite  53, 72
N6-Me-A-CE Phosphoramidite  141N6-Me-dA-CE Phosphoramidite  53, 72
Pac-A-CE Phosphoramidite  135Pac-A-RNA-CPG  135Pac-dA-CE Phosphoramidite  27

A-2-Amino

2-Amino-A-TOM-CE Phosphoramidite  1372-Amino-dA-CE Phosphoramidite  532'-OMe-2-Amino-A-CE Phosphoramidite  146Pac-2-Amino-dA-CE Phosphoramidite  53

Abasic Site 68, 90

Abasic II Phosphoramidite  68
dSpacer Phosphoramidite 68
Pyrrolidine-CE Phosphoramidite  69

Acridine Labelling

3’-Acridine CPG  120Acridine Phosphoramidite 120

Activator

4,5-Dicyanoimidazole  34
5-Benzylthio-1H-tetrazole  34
5-Ethylthio-1H-tetrazole  30, 34, 77, 116, 118
Activator (Powder)  34
Saccharin 1-Methylimidazole  34
Tetrazole  12, 23

Adamantane Carbonyl Chloride 43
Affinity Chromatography 157
Aldehyde Modifier

5'-Aldehyde-Modifier C2 Phosphoramidite  895-Formyl-dC-CE Phosphoramidite  56
Formylindole CE Phosphoramidite  89

Alternative Solvents and Reagents 34
Amino-dA
8-Amino-dA-CE Phosphoramidite  65

Amino-dG

8-Amino-dG-CE Phosphoramidite  68

Amino-Modifiers

3'-Amino-Modifier C6 dC CPG  87
3'-Amino-Modifier C6 dT CPG  87
3’-Amino-Modifier Serinol CPG  85
3'-PT-Amino-Modifier C3 CPG  85
3'-PT-Amino-Modifier C6 CPG  85
3'-PT-Amino-Modifier C6 PS  85
5'-Amino-dT-CE Phosphoramidite  615'-Amino-Modifier 5  80
5'-Amino-Modifier C3-TFA  80, 81
5'-Amino-Modifier C6  80, 81
5’-Amino-Modifier C6-PDA  81
5'-Amino-Modifier C6-TFA  80, 81
5'-Amino-Modifier C12  80
5’-Amino-Modifier C12-PDA  81
5’-Amino-Modifier TEG  80
5’-Amino-Modifier-TEG-PDA  81
5’-DMS(O)MT-Amino-Modifier C6  80
Amino-Modifier C2 dT  83
Amino-Modifier C6 dA  83
Amino-Modifier C6 dC  83
Amino-Modifier C6 dT  83
Amino-Modifier C6-U Phosphoramidite  138Amino-Modifier Serinol Phosphoramidite  84

MISCELLANEOUS

Index

169

INDEX
Fmoc-Amino-Modifier C6 dT  84
N2-Amino-Modifier C6 dG  83
PC Amino-Modifier Phosphoramidite  82, 92, 101

5’-Biotin II Phosphoramidite  1065’-Biotin Phosphoramidite  106Biotin-dT  106Biotin Phosphoramidite  105BiotinTEG Azide  98
BiotinTEG Phosphoramidite  105DesthiobiotinTEG Azide  98
DesthiobiotinTEG-CPG  107DesthiobiotinTEG Phosphoramidite  106PC Biotin NHS Ester  92
PC Biotin Phosphoramidite  92, 106
Protected BiotinLC Serinol Phosphoramidite  101, 105Protected Biotin Serinol Phosphoramidite  100, 105

AminoOxy-Modifier

5’-AminoOxy-Modifier 11  82

Aminopurine

2'-OMe-2-Aminopurine-CE Phosphoramidite  146

Anthraquinone

3’-Uaq Cap CPG  55

Applied Biosystems Instruments

AB 3900 1000Å CPG Columns  10
AB 3900 Polystyrene Columns  10
AB 3900 Polystyrene Modifier Columns  11
CE Phosphoramidites 8
Solvents/Reagents 8
Supports and Columns 9

Aptamer Development 79
AquaPhluor® 593

BlackBerry® Quencher

3’-BBQ-650® CPG  1185’-BBQ-650® Phosphoramidite  118BBQ-650®-dT  118

Black Hole Quencher™ Dyes

3'-BHQ-1 CPG  1173'-BHQ-2 CPG  1173'-BHQ-3 CPG  117, 118
5’-BHQ-1 Phosphoramidite  1165’-BHQ-2 Phosphoramidite  77, 116, 118
BHQ-1-dT  116, 118
BHQ-2-dT  116

5’-AquaPhluor® 593 Phosphoramidite  114AquaPhluor® 593 CPG  115

AquaPhluor® 639

5’-AquaPhluor® 639 Phosphoramidite  114AquaPhluor® 639 CPG  115

Asymmetric Doubler (LEV) Phosphoramidite 91
Aza-dC
5-Aza-5,6-dihydro-dC-CE Phosphoramidite  78

Azides

6-FAM-TEG Azide  98
6-HEX Azide  98
6-TET Azide  98
BiotinTEG Azide  98
Coumarin Azide  98
DesthiobiotinTEG Azide  98
Dipivaloyl 6-FAM-TEG Azide  98
Disulfo-Cyanine 7 Azide  99
Psoralen Azide  99
TEMPO Azide  99
TEMPO-TEG Azide  99

Azidobutyrate NHS Ester 95
Azido-Modifier Serinol CPG 102
Azobenzene
Azobenzene Phosphoramidite  129

BBenzylthio-1H-tetrazole 34
beta-L-DNA 46
Biocompatible Chemical Ligation 70
Biotin Labelling
3’-BiotinTEG CPG  1073’-BiotinTEG PS  1073’-Protected BiotinLC Serinol CPG  1073’-Protected Biotin Serinol CPG  101, 107

170

Brancher Phosphoramidite

dC Brancher Phosphoramidite 91

Br-dA

8-Br-dA-CE Phosphoramidite  66

Br-dC

5-Br-dC-CE Phosphoramidite  66

Br-dG

8-Br-dG-CE Phosphoramidite  66

Br-dU

5-Br-dU-CE Phosphoramidite  66
5-Br-dU-CPG  66

Bromohexyl Phosphoramidite 95
Br-U

2'-OMe-5-Br-U-CE Phosphoramidite  1465-Br-U-CE Phosphoramidite  139

CC

2’,3’-ddC  62
2’,3'-ddC-CPG  62
2’-F-Bz-C-ANA CE Phosphoramidite  1502'-OMe-5-Me-C-CE Phosphoramidite  1462'-OMe-Ac-C-CE Phosphoramidite  143, 144
2’-OMe-Ac-C-PACE Phosphoramidite  1512'-OMe-Ac-C-RNA  1452'-OMe-C-RNA  1453'-Amino-Modifier C6 dC CPG  87
3'-dC-CE Phosphoramidite  71
3'-dC-CPG  61, 71
5-Br-dC-CE Phosphoramidite  66

INDEX

Caged 77

DEACM-Caged-dG-CE Phosphoramidite  77
NPOM-Caged-dT-CE Phosphoramidite  77

Camphorsulfonyloxaziridine (CSO) 36
Cap CPG
3’-Uaq Cap CPG  55, 70

Cap Phosphoramidite

5’-Pyrene Cap Phosphoramidite  55
5’-Trimethoxystilbene Cap Phosphoramidite  55

Capping Reagent

UniCap Phosphoramidite 36

Carboxy-dC

5-Carboxy-dC-CE Phosphoramidite  56

Carboxy-Modifiers5’-Carboxy-Modifier C5  82
5'-Carboxy-Modifier C10  82
Carboxy-dT  83

Chain Terminators 62
Chelates

EDTA-C2-dT-CE Phosphoramidite  125

Chemical Phosphorylation 88

Cholesterol Labelling

3’-Cholesteryl-TEG CPG  1215’-Cholesteryl-TEG Phosphoramidite  121Cholesteryl-TEG Phosphoramidite  81, 121

CleanAmp™ Technology
CleanAmp™ Primers 60

Click Chemistry 93

1,2,3-triazoles  93
1-Ethynyl-dSpacer CE Phosphoramidite  96
3’-Alkyne-Modifier Serinol CPG  86, 95, 103
3’-Propargyl-5-Me-dC CPG  70
5’-Bromohexyl Phosphoramidite  95
5-Ethynyl-dU-CE Phosphoramidite  94
5’-Hexynyl Phosphoramidite  95
5’-I-dT-CE Phosphoramidite  95
Alkyne-Modifier Serinol Phosphoramidite  95, 101
Alkyne-NHS Ester  95
Azides  95
Azidobutyrate NHS Ester  95
baseclick Oligo-Click-M-Biotin  96
baseclick Oligo-Click-M-Fluorescein  96
baseclick Oligo-Click-M-Reload  96
baseclick Oligo-Click-M-TAMRA  96
C8-Alkyne-dC-CE Phosphoramidite  93, 96
C8-Alkyne-dT-CE Phosphoramidite  93
C8-TIPS-Alkyne-dC-CE Phosphoramidite  94
C8-TIPS-Alkyne-dT-CE Phosphoramidite  94
C8-TMS-Alkyne-dC-CE Phosphoramidite  93, 94
C8-TMS-Alkyne-dT-CE Phosphoramidite  94
Click DNA and RNA Ligation  70
Copper-free Click Chemistry  95
THPTA Ligand 94
TIPS-5-Ethynyl-dU-CE Phosphoramidite  94

Convertible 2-dG

2-F-dI-CE Phosphoramidite  73

Convertible dA

O6-Phenyl-dI-CE Phosphoramidite  73

Convertible dU

O4-Triazolyl-dU-CE Phosphoramidite  73

Convertible F-dC

TMP-F-dU-CE Phosphoramidite  73

Convertible Nucleosides 73
Copper-free Click Chemistry 96
5’-DBCO-TEG Phosphoramidite  97
DBCO-dT-CE Phosphoramidite  97
DBCO-sulfo-NHS Ester  97

Cross-linking 64, 66, 99, 124, 130
Custom Doping 57
Cyanine Labelling

MISCELLANEOUS

5-Carboxy-dC-CE Phosphoramidite  56
5-Formyl-dC-CE Phosphoramidite  56
5-Hydroxymethyl-dC-CE Phosphoramidite  56
5-Hydroxymethyl-dC II-CE Phosphoramidite  56
5-I-dC-CE Phosphoramidite  66
5-Me-Bz-C-LNA-CE Phosphoramidite  44
5-Me-C-2'-MOE-Phosphoramidite  1485-Me-dC-CE Phosphoramidite  52
5-OH-dC-CE Phosphoramidite  67
Ac-C-CE Phosphoramidite  134Ac-C-RNA-CPG  131, 133, 136
Ac-dC-5’-CE Phosphoramidite  38
Ac-dC-CE Phosphoramidite  8, 12, 15, 16, 18, 20, 22, 27
Ac-dC-Me Phosphonamidite  40
Ac-dC-PACE Phosphoramidite  41
Amino-Modifier C6 dC  83
AP-dC  74AP-dC-CE Phosphoramidite  52
C8-Alkyne-dC-CE Phosphoramidite  93, 96
C8-TMS-Alkyne-dC-CE Phosphoramidite  93
C-TOM-CE Phosphoramidite  132Cyanine Labelling
sulfoCyanine 3 NHS Ester 113
dC Brancher Phosphoramidite 91
dC-CE Phosphoramidite  8, 12, 15, 16, 18, 20, 22
dC-H-Phosphonate  43
dC-Me Phosphoramidite  42
dC-Thiophosphoramidite  147N4-Et-dC-CE Phosphoramidite  53
pdC-CE Phosphoramidite  52
Pyrrolo-dCTP  74
tC-CE Phosphoramidite  76
tC°-CE Phosphoramidite  76

Cyanine 3.5 Phosphoramidite  112Cyanine 3 CPG  113Cyanine 3 Phosphoramidite  112Cyanine 5.5 Phosphoramidite  112Cyanine 5 CPG  113Cyanine 5 Phosphoramidite  112

171

INDEX
Disulfo-Cyanine 7 Azide  113sulfoCyanine 3 NHS Ester  113sulfoCyanine 5 NHS Ester  113

Cyanovinylcarbazole

3-Cyanovinylcarbazole Phosphoramidite  130CNVK 130

Pac-2-Amino-dA-CE Phosphoramidite  53

Dicyanoimidazole 34
Dideoxynucleoside, 2',3'- 61
Dideoxynucleosides
2’,3’-ddA-CE Phosphoramidite  62
2’,3’-ddC-CE Phosphoramidite  622’,3'-ddC-CPG  62
2’,3’-ddG-CE Phosphoramidite  62
2’,3’-ddT-CE Phosphoramidite  62

Cyclo-dA

5’,8-Cyclo-dA CE Phosphoramidite  69

Cyclo-dG5’,8-Cyclo-dG CE Phosphoramidite  69

Cyclooctatetraene

COT Serinol Phosphoramidite 103

Dihydro-dT

5,6-Dihydro-dT-CE Phosphoramidite  67

Dihydro-dU

5,6-Dihydro-dU-CE Phosphoramidite  67

D
Dabcyl Labelling

3'-Dabcyl CPG  1043'-Dabcyl PS  1043'-Dabsyl CPG  77, 104, 116, 118
5’-Dabcyl Phosphoramidite  104Dabcyl-dT  104

DBCO

5’-DBCO-TEG Phosphoramidite  97
DBCO-dT-CE Phosphoramidite  97
DBCO-Serinol Phosphoramidite  97
DBCO-sulfo-NHS Ester  97

DEACM-Caged-dG-CE Phosphoramidite 77
Deaza-8-aza-A
7-deaza-8-Aza-A-CE Phosphoramidite  1407-Deaza-8-aza-dA-CE Phosphoramidite  63

Deaza-8-aza-G

7-deaza-8-Aza-dG-CE Phosphoramidite  63

Deaza-A

Dithiol

3’-Dithiol Serinol CPG  86
Dithiol Serinol Phosphoramidite 82

DNA Damage/Repair 68–69, 69
DNA Methylation

5-Carboxy-dC-CE Phosphoramidite  56
5-Formyl-dC-CE Phosphoramidite  56
5-Me-dC-CE Phosphoramidite  52

DNA Methyltransferases 78
DNP Labelling
DNP-TEG Phosphoramidite  120

Doubler Phosphoramidite
Symmetric  91

Dr. Oligo Synthesizers

CE Phosphoramidites 20
Solvents and Reagents 20

dSpacer 90
Duplex Stabilization

Bases Affecting Duplex Stability  52
Caps for Increased Duplex Stability/Base-Pairing Fidelity  55
Duplex Stability Modification  52

3-Deaza-dA-CE Phosphoramidite  63
7-Deaza-dA-CE Phosphoramidite  63

Deaza-G

7-Deaza-dG-CE Phosphoramidite  63

Deaza-X

7-Deaza-dX-CE Phosphoramidite  50  63

Dendrimers

Asymmetric Doubler (LEV) Phosphoramidite  91
Long Trebler Phosphoramidite  91
Symmetric Doubler Phosphoramidite  91
Trebler Phosphoramidite  91

Depurination Resistant CE Phosphoramidites 26
Desthiobiotin
DesthiobiotinTEG-CPG  107DesthiobiotinTEG Phosphoramidite  106

Deuterated Nucleosides 66
Diaminopurine

2,6-Diaminopurine-TOM-CE Phosphoramidite  1372-Amino-dA-CE Phosphoramidite  53
2’-OMe-2,6-Diaminopurine CE Phosphoramidite  146

172

EEclipse® Quencher

Eclipse® Quencher CPG  115Eclipse® Quencher Phosphoramidite  114MGB Eclipse® CPG  124

EDTA-dT

EDTA-C2-dT-CE Phosphoramidite  125

EdU

5-Ethynyl-dU-CE Phosphoramidite  94
TIPS-5-Ethynyl-dU-CE Phosphoramidite  94

ELITechGroup Dyes and Quencher 114
5’-CDPI3 MGB™ Phosphoramidite  123MGB Eclipse® CPG  124

Epigenetics 56, 141

INDEX
EstersAlkyne-NHS Ester  95
Azidobutyrate NHS Ester  95
DBCO-sulfo-NHS Ester  97
Fluorescein NHS ester 109
Methylene Blue NHS Ester  126ROX NHS Ester  119sulfoCyanine 3 NHS Ester  113sulfoCyanine 5 NHS Ester  113TAMRA NHS Ester 119
Thiazole Orange NHS Ester  127

5’-Tetrachloro-Fluorescein  1086-Fluorescein Phosphoramidite  1096-Fluorescein Serinol Phosphoramidite  100, 109
Dichloro-diphenyl-fluorescein  111Fluorescein-dT Phosphoramidite  109Fluorescein NHS ester 109
JOE-dT Phosphoramidite  109SIMA (HEX)  111

Fluorescein NHS ester 109
Fluorescent Nucleosides 74

2-Aminopurine-CE Phosphoramidite  64
5-Me-2'-deoxyZebularine-CE Phosphoramidite  78
AP-dC-CE Phosphoramidite  52
Etheno-dA-CE Phosphoramidite  74
Perylene-dU-CE Phosphoramidite  75
Pyrrolo-C-TOM-CE Phosphoramidite  138Pyrrolo-dC-CE Phosphoramidite  74
Pyrrolo-dCTP  74
tC-CE Phosphoramidite  76
tC°-CE Phosphoramidite  76

Et-dC-CE Phosphoramidite 53
Etheno-A
Etheno-dA-CE Phosphoramidite  74

Ethylthiotetrazole 34
Excimers 128
Expedite™ Instruments

CE Phosphoramidites 12, 22
Solvents and Reagents 12, 23
Supports and Columns 13, 24

Formyl-dC

5-Formyl-dC-CE Phosphoramidite  56
5-Formyl-dC III-CE Phosphoramidite  56

FAM

3’-(6-FAM) CPG  1103'-(6-FAM) PS  1106-FAM  1086-FAM-TEG Azide  98
Dipivaloyl 6-FAM-TEG Azide  98

Formylindole CE Phosphoramidite 89
Free Radicals 67
F-RNA Monomers
2'-F-Ac-C-CE Phosphoramidite  148, 149
2'-F-A-CE Phosphoramidite  1492'-F-G-CE Phosphoramidite  1492'-F-I-CE Phosphoramidite  1492'-F-U-CE Phosphoramidite  149

F-ANA Monomers

2’-F-A-ANA CE Phosphoramidite  1502’-F-Ac-C-ANA CE Phosphoramidite  1502’-F-Bz-C-ANA CE Phosphoramidite  1502’-F-G-ANA CE Phosphoramidite  1502’-F-U-ANA CE Phosphoramidite  150

F-C

2'-F-Ac-C-CE Phosphoramidite  55
F-dC Precursor  73

F-dI

2-F-dI-CE Phosphoramidite  73

F-dU

5-F-dU-CE Phosphoramidite  66
5-Fluoro-dU  66

Ferrocene Labelling

Ferrocene-dT-CE Phosphoramidite  125

Fluorescein Labelling3’-(6-FAM) CPG  1103’-(6-FAM) PS  1103’-(6-Fluorescein) CPG  110, 113
3’-6-Fluorescein Serinol CPG  102, 110
3’-Fluorescein CPG  1103'-Fluorescein-dT CPG  1105’-Dichloro-dimethoxy-Fluorescein  1095’-Fluorescein Phosphoramidite  1085’-Hexachloro-Fluorescein  108

F-U

2'-OMe-5-F-U-CE Phosphoramidite  146

GG

2’,3’-ddG  62
2’-F-G-ANA CE Phosphoramidite  1502'-F-G-CE Phosphoramidite  1492'-OMe-G-CE Phosphoramidite  1432’-OMe-G-PACE Phosphoramidite  1512'-OMe-G-RNA  1452'-OMe-iPr-Pac-G-CE Phosphoramidite  1443'-dG-CE Phosphoramidite  71
3'-dG-CPG  61, 72
6-Thio-dG-CE Phosphoramidite  64
6-Thio-G-CE Phosphoramidite  1397-Deaza-8-aza-dG-CE Phosphoramidite  63
7-Deaza-dG-CE Phosphoramidite  63
8-Amino-dG-CE Phosphoramidite  68
8-Br-dG-CE Phosphoramidite  66
8-Oxo-dG-CE Phosphoramidite  67
Ac-G-CE Phosphoramidite  134Ac-G-RNA-CPG  133, 136
dG-CE Phosphoramidite  8, 12, 15, 16, 18, 20, 22

MISCELLANEOUSF

173

INDEX
dG-H-Phosphonate  43
dG-Me Phosphonamidite  40
dG-Me Phosphoramidite  42
dG-PACE Phosphoramidite  41
dG-Thiophosphoramidite  147dmf-dG-5’-CE Phosphoramidite  38
dmf-dG-CE Phosphoramidite  8, 12, 15, 16, 18, 20, 22
dmf-G-LNA-CE Phosphoramidite  44G-2'-MOE-Phosphoramidite  148G-TOM-CE Phosphoramidite  132iPr-Pac-dG-CE Phosphoramidite  27
iPr-Pac-G-RNA-CPG  136N2-Amino-Modifier C6 dG  83
O6-Me-dG-CE Phosphoramidite  72

GalNAc5’-GalNAc C3 Phosphoramidite  122GalNAc C3 CPG 122

G-Clamp 52, 74
GE Healthcare LIfe Sciences Instruments
CE Phosphoramidite 18
Solvents and Reagents 19

Hexynyl Phosphoramidite 95
High Load CPG 33
H-Phosphonate Chemistry
Monomers 43, 46
Reagents for ABI synthesizers  43

Hydrogen Bonding 63
Hydroxy-C

5-OH-dC-CE Phosphoramidite  67

Hydroxymethyl-dC

5-Hydroxymethyl-dC-CE Phosphoramidite  56
5-Hydroxymethyl-dC II-CE Phosphoramidite  56

Hydroxymethyl-dU

5-Hydroxymethyl-dU-CE Phosphoramidite  67

Hydroxy-U

5-OH-dU-CE Phosphoramidite  67

I
I

Glen Gel-Pak™ Purification
Glen Gel-Pak™  156

Glen-Pak™ Purification

Adapter Rack 154
Glen-Pak™ DNA Purification Cartridge  153Glen-Pak™ RNA Purification Cartridge  154RNA Quenching Buffer  154Seal for Adapter Rack 154

Glen UnySupport™

Glen UnySupport CPG  28
Glen UnySupport PS  29

Glyceryl CPG 86
Gold

2-F-dI-CE Phosphoramidite  732'-OMe-I-CE Phosphoramidite  147dI-CE Phosphoramidite  57
dI-CPG  57
I-CE Phosphoramidite  139O6-Phenyl-dI-CE Phosphoramidite  73

I-dC

5-I-dC-CE Phosphoramidite  66

I-dT

5'-I-dT-CE Phosphoramidite  95

I-dU

5-I-dU-CE Phosphoramidite  66

Hi-Motif DNA structures 79
Introduction 1, 3, 5, 6, 8, 10, 12, 14, 16, 18, 20,
22, 24
Ionizing Radiation 67
isodC

Halogenated Nucleosides

isodG

Conjugation to gold surfaces  100

G-Quadruplex 79

2'-OMe-5-F-U-CE Phosphoramidite  1465-Br-dC-CE Phosphoramidite  66
5-Br-dU-CE Phosphoramidite  66
5-Br-dU-CPG  66
5-Br-U-CE Phosphoramidite  1395-F-dU-CE Phosphoramidite  66
5-I-dC-CE Phosphoramidite  66
5-I-dU-CE Phosphoramidite  66
5-I-U-CE Phosphoramidite  1398-Br-dA-CE Phosphoramidite  66
8-Br-dG-CE Phosphoramidite  66

HEX 108

6-HEX Azide  98, 99

Hexylammonium Acetate (HAA) 155
174

dmf-5-Me-isodC-CE Phosphoramidite  59
dmf-isodG-CE Phosphoramidite  59

Isopropyl Phosphite 43
I-U

5-I-U-CE Phosphoramidite  139

JJOE

5’-Dichloro-dimethoxy-Fluorescein Phosphoramidite II  109

JOE-dT Phosphoramidite 109

INDEXK
dK-CE Phosphoramidite  58

K & A INSTRUMENTS 23

L
Labelling of MicroRNAs 70
Large Scale Synthesis
N3-Cyanoethyl-dT  78

beta-L-DNA monomers 46
Locked Analog Phosphoramidites
5-Me-Bz-C-LA-CE Phosphoramidite  44
Bz-A-LA-CE Phosphoramidite  44
dmf-G-LA-CE Phosphoramidite  44
T-LA-CE Phosphoramidite  44

Locked Nucleic Acid (LNA) 44
Long Trebler Phosphoramidite 91

MGB Eclipse® CPG 124
MicroRNA 70
Minor 2’-OMe-RNA Phosphoramidites 146–148
Minor Groove 64
Minor Groove Binder (MGB) 123
Mixed Base Combinations 57
Modifiers 80, 81, 84
Mutagenesis 72

N
Nebularine

2'-DeoxyNebularine-CE Phosphoramidite  57

Nitroindole

5-Nitroindole-CE Phosphoramidite  58

M

Non-canonical Structures 79

2’-MOE RNA 148
Maleimide-Modifier

O

Me-C

OMe-RNA Synthesis

5’-Maleimide-Modifier Phosphoramidite  82
Maleimide NHS Ester (SMCC)  82
2'-OMe-5-Me-C-CE Phosphoramidite  1463’-Propargyl-5-Me-dC CPG  70
5-Me-C-TOM-CE Phosphoramidite  1375-Me-dC-CE Phosphoramidite  52
Ac-5-Me-dC-CE Phosphoramidite  52

MerMade Instruments
CE Phosphoramidites 16
Solvents and Reagents 16
Supports and Columns 17

Methacrylate C6 Phosphoramidite 80
Methylated Nucleosides
1-Me-A-CE Phosphoramidite  1411-Me-dA-CE Phosphoramidite  72
1-Me-Pseudouridine Phosphoramidite  141N6-Ac-N6-Me-dA-CE Phosphoramidite  53, 72
N6-Me-A-CE Phosphoramidite  141N6-Me-dA-CE Phosphoramidite  53, 72
O4-Me-dT-CE Phosphoramidite  53, 72
O6-Me-dG-CE Phosphoramidite  72

Methylene Blue

Methylene Blue II Phosphoramidite  126Methylene Blue NHS Ester  126

Methyl Phosphonamidites 40
Me-U

2'-OMe-5-Me-U-CE Phosphoramidite  1465-Me-U-CE Phosphoramidite  139

MGB

Oligo-Affinity Support
OAS PS 157

2’-OMe-RNA Phosphoramidites  1432’-OMe-RNA Supports  145Minor 2’-OMe-RNA Phosphoramidites  146

OMe-T 146
Oxo-dA

8-Oxo-dA-CE Phosphoramidite  67

Oxo-dG

8-Oxo-dG-CE Phosphoramidite  67

PP

dP-CE Phosphoramidite  58, 60

PACE Phosphoramidites

2’-OMe-RNA-PACE Phosphoramidites  151DNA PACE phosphoramidites 41

Palmitate Labeling 122

Palmitate Phosphoramidite 122

MISCELLANEOUS

K

3’-CDPI3 MGB™ CPG  54
5’-CDPI3 MGB™ Phosphoramidite  54, 123
CDPI3 MGB™ CPG 123
MGB Eclipse® CPG  124

PC Biotin NHS Ester 92
PCR/Sequencing Utilities 57
Perylene

Perylene-dU-CE Phosphoramidite  75, 128

PhenothiazinetC-CE Phosphoramidite  76

Phenoxazine

tC°-CE Phosphoramidite  76

Phosphonocarboxylate Monomers 41
175

INDEX
Phosphorylation

3’-CPR II CPG  89
3'-Phosphate CPG  88
3'-Phosphate PS  88
Chemical Phosphorylation Reagent  88
Chemical Phosphorylation Reagent II  89
CPR II 88
Solid CPR II 88

Photoaffinity Labelling 64
Photocleavable Monomers

PC Amino-Modifier Phosphoramidite  82, 92, 101
PC Biotin Phosphoramidite  92, 106
PC Linker Phosphoramidite 92
PC Spacer Phosphoramidite 90, 92

Photo cross-linking 64, 130
Photo-Regulation of DNA Function 77
DEACM-Caged-dG-CE Phosphoramidite  77
NPOM-Caged-dT-CE Phosphoramidite  77

Purine 58

Puromycin

Puromycin CPG  128

Pyrene5’-Pyrene Cap Phosphoramidite  55
Pyrene-dU-CE Phosphoramidite  75, 76, 77, 128

Pyridin-2-one-CE Phosphoramidite 140
Pyrrolidine-CE Phosphoramidite 69
Pyrrolo-C
Pyrrolo-C-TOM-CE Phosphoramidite  138Pyrrolo-dC-CE Phosphoramidite  74
Pyrrolo-dCTP  74

Q
Q-Supports 31, 32
Quasar 113

Quasar 570-dT Phosphoramidite  113Quasar 670-dT Phosphoramidite  113

Photo-responsive DNA

Azobenzene Phosphoramidite  129

Phthalimide (PT)3'-PT-Amino-Modifier C3 CPG  85
3'-PT-Amino-Modifier C6 CPG  85
3'-PT-Amino-Modifier C6 PS  85

Quenched Autoligation (QUAL) Probes
5’-Dabsyl-dT-CE Phosphoramidite  130

R

Poly-Pak™ Purification

Redmond Red®

Polystyrene Supports

Repair Enzyme 67
Reverse Synthesis 38
Rhodamine 119
Ribo-tCO-CE Phosphoramidite 142
RNA Supports

Poly-Pak™ Cartridge  155Poly-Pak™ II Cartridge  155Poly-Pak™ Packing  154, 155
Reagents 154, 155
3'-(6-FAM) PS  1103'-BiotinTEG PS  1073'-Dabcyl PS  1043'-Phosphate PS  88
3'-PT-Amino-Modifier C6 PS  85
3'-TAMRA PS  119Glen UnySupport PS  28
Universal Support III PS 30

Redmond Red® CPG  115Redmond Red® Phosphoramidite  114

for 3’ DNA Modification  131

RNA Synthesis

2’-MOE RNA Phosphoramidites  1482’-OMe-RNA SYNTHESIS  143Minor RNA Phosphoramidites 136, 141
RNA Phosphoramidites 134, 135
RNA Supports 135, 136
RNA Supports for TOM-RNA Synthesis  132, 133
TOM-Protected Minor RNA Phosphoramidites  133, 137,
138, 139
TOM-Protected RNA Phosphoramidites  132

PPG 63
Propyne Derivatives

pdC-CE Phosphoramidite  52
pdU-CE Phosphoramidite  52

Protein-DNA Interaction 64
PseudoU

1-Me-Pseudouridine Phosphoramidite  1412’-deoxypseudoU-CE Phosphoramidite  64
PseudoUridine-CE Phosphoramidite  140

Psoralen LabellingPsoralen Azide  99, 124
Psoralen C2 Phosphoramidite 124
Psoralen C6 Phosphoramidite 124

Purification

Glen-Pak™ Purification  153, 154
Poly-Pak™ Purification  155

Purine176

ROX NHS Ester 119

S
Saccharin 1-Methylimidazole 34
SBC Oligos 54
Sequence Modifiers 84
Serinol Backbone

3’-6-Fluorescein Serinol CPG  102, 110
3’-Alkyne-Modifier Serinol CPG  86, 95, 103

INDEXSIMASIMA (HEX)-dT Phosphoramidite  111SIMA (HEX) Phosphoramidite  111

SMI 34
Spacer Modifiers

1-Ethynyl-dSpacer CE Phosphoramidite  96
3'-Spacer C3 CPG  90dSpacer-5'-CE Phosphoramidite  90dSpacer CE Phosphoramidite 90
PC Spacer Phosphoramidite 90, 92
rSpacer TBDMS CE Phosphoramidite 140
Spacer C12 CE Phosphoramidite 90
Spacer Phosphoramidite 9 90
Spacer Phosphoramidite 18 90
Spacer Phosphoramidite C3 90

Spermine Phosphoramidite 54
Spin Labels
TEMPO Azide  99
TEMPO-TEG Azide  99

5’-Dabsyl-dT  1305'-I-dT-CE Phosphoramidite  955'-OMe-dT-CE Phosphoramidite  61
Amino-Modifier C2 dT  83
Amino-Modifier C6 dT  83
C8-Alkyne-dT-CE Phosphoramidite  93
C8-TIPS-Alkyne-dT-CE Phosphoramidite  94
C8-TMS-Alkyne-dT-CE Phosphoramidite  94
DBCO-dT-CE Phosphoramidite  97
dT-CE Phosphoramidite  8, 12, 15, 16, 18, 20, 22
dT-H-Phosphonate  43
dT-Me  Phosphonamidite  40
dT-Me Phosphoramidite  42dT-PACE Phosphoramidite  41
EDTA-C2-dT-CE Phosphoramidite  125Ferrocene-dT-CE Phosphoramidite  125Fluorescein-dT  109N3-Cyanoethyl-dT  78
NPOM-Caged-dT  77
O4-Me-dT-CE Phosphoramidite  53, 72
S-Bz-Thiol-Modifier C6-dT  84
TAMRA-dT  119Thymidine Glycol CE Phosphoramidite  68
T-LNA-CE Phosphoramidite  44

TAMRA Labelling

3'-TAMRA CPG  1193'-TAMRA PS  119TAMRA-dT  119TAMRA NHS Ester 119

tC

tC-CE Phosphoramidite  76

Stearyl Labelling 121

tCnitroSterlingtCo

5’- Stearyl Phosphoramidite  121Introduction  7

Structural Studies 63
Structure/Activity Relationship 63
sulfoCyanine 3 NHS Ester 113
sulfoCyanine 5 NHS Ester 113
Sulfurizing Reagent 37
Sulfurizing Reagent II 37
Symmetric Doubler Phosphoramidite 91

TT

2’,3’-ddT  62
2-Thio-dT-CE Phosphoramidite  64
3’-Amino-dT CPG  70
3'-Amino-Modifier C6 dT CPG  87
3'-dT-CE Phosphoramidite  71
3'-dT-CPG  61, 72
3'-Fluorescein-dT CPG  1104-Thio-dT-CE Phosphoramidite  64
5,6-Dihydro-dT-CE Phosphoramidite  675'-Amino-dT-CE Phosphoramidite  61

tCnitro-CE Phosphoramidite  76
Ribo-tC°-CE Phosphoramidite  142tC°-CE Phosphoramidite  76

TEMPO

TEMPO Azide  99
TEMPO-TEG Azide  99

Termination, 3'2’,3’-ddA  62
2’,3’-ddC  62
2’,3'-ddC-CPG  62
2’,3’-ddG  62
2’,3’-ddT  62
3'-3' linkage  39, 61
3'-dA-CPG  61
3'-dC-CPG  61
3'-dG-CPG  61
3'-dT-CPG  61
3'-Spacer C3 CPG  90

MISCELLANEOUS

3’-Amino-Modifier Serinol CPG  85, 102
3’-Azido-Modifier Serinol CPG  1023’-Dithiol Serinol CPG  86, 103
3’-Protected Biotin Serinol CPG  101, 107
6-Fluorescein Serinol Phosphoramidite  100, 109
Alkyne-Modifier Serinol Phosphoramidite  95
Amino-Modifier Serinol Phosphoramidite  84, 101
COT Serinol Phosphoramidite 103
Dithiol Serinol Phosphoramidite 82, 101
Protected BiotinLC Serinol Phosphoramidite  101, 106
Protected Biotin Serinol Phosphoramidite  100, 106

Termination, 5'5'-OMe-dT-CE Phosphoramidite  61

Terminus Modifiers 80
TET 108177

INDEX
6-TET Azide  98, 99

Thiazole Orange 127
Thio-dT

2-Thio-dT-CE Phosphoramidite  64
4-Thio-dT-CE Phosphoramidite  64

Thio-dU

4-Thio-dU-CE Phosphoramidite  64

Thio-G

6-Thio-dG-CE Phosphoramidite  64
6-Thio-G-CE Phosphoramidite  139

Thiol-Modifiers3’-Dithiol Serinol CPG  86
3’-Thiol-Modifier 6 S-S CPG  86
5’-Thiol-Modifier C6  82
Dithiol Serinol Phosphoramidite 82
S-Bz-Thiol-Modifier C6-dT  84
Thiol-Modifier C6 S-S  82

Thiophosphoramidites

2’-OMe-RNA Thiophosphoramidites  147

Thio-U

4-Thio-U-TOM-CE Phosphoramidite  137

Thymidine Glycol

Thymidine Glycol CE Phosphoramidite  68

Thymine Dimer

Cis-syn Thymine Dimer Phosphoramidite  69

Tm Modulation 59
Tocopherola-Tocopherol-TEG Phosphoramidite  121

TOM-Protecting-GroupAc-A-RNA-CPG  132Ac-C-RNA-CPG  133Ac-G-RNA-CPG  133A-TOM-CE Phosphoramidite  132C-TOM-CE Phosphoramidite  132G-TOM-CE Phosphoramidite  132U-RNA-CPG  133U-TOM-CE Phosphoramidite  132

Trebler Phosphoramidite
Trebler  91

Trimer phosphoramidites 48
Trimethoxystilbene

5’-Trimethoxystilbene Cap Phosphoramidite  55

Triphosphate Nucleotides
Pyrrolo-dCTP  74

Triplex 63
Triplex-forming oligonucleotides 79

U
U

2'-OMe-5-F-U-CE Phosphoramidite  1462'-OMe-5-Me-U-CE Phosphoramidite  1462'-OMe-U-CE Phosphoramidite  1432’-OMe-U-PACE Phosphoramidite  1512'-OMe-U-RNA  1453’-Uaq Cap CPG  55, 70
4-Thio-dU-CE Phosphoramidite  64
5,6-Dihydro-dU-CE Phosphoramidite  67
5-Br-dU-CE Phosphoramidite  66
5-Br-dU-CPG  66
5-Ethynyl-dU-CE Phosphoramidite  94
5-F-dU-CE Phosphoramidite  66
5-Hydroxymethyl-dU-CE Phosphoramidite  67
5-I-dU-CE Phosphoramidite  66
5-I-U-CE Phosphoramidite  1395-Me-U-2'-MOE-Phosphoramidite  1485-OH-dU-CE Phosphoramidite  67
Amino-Modifier C6-U Phosphoramidite  138Br-U-CE Phosphoramidite  139dU-CE Phosphoramidite  57
dU-CPG 500  57
dU-CPG 1000  57
O4-Triazolyl-dU-CE Phosphoramidite  73
pdU-CE Phosphoramidite  52
Perylene-dU-CE Phosphoramidite  75
Pyrene-dU-CE Phosphoramidite  75, 76, 77
TIPS-5-Ethynyl-dU-CE Phosphoramidite  94
TMP-F-dU-CE Phosphoramidite  73
U-CE Phosphoramidite  134, 135
U-RNA-CPG  131, 133, 136
U-TOM-CE Phosphoramidite  132

UltraMILD Deprotection

2'-OMe-Ac-C-CE Phosphoramidite  1442'-OMe-iPr-Pac-G-CE Phosphoramidite  1442'-OMe-Pac-A-CE Phosphoramidite  144Ac-C-CE Phosphoramidite  135Ac-dC-CE Phosphoramidite  27
Cap Mix A  27, 42, 136, 144
iPr-Pac-dG-CE Phosphoramidite  27
iPr-Pac-G-CE Phosphoramidite  135Pac-A-CE Phosphoramidite  135Pac-dA-CE Phosphoramidite  27
Potassium Carbonate in Methanol  27, 42, 136, 144

UniCap Phosphoramidite 36
Universal Phosphoramidite 81
Universal Support III
Universal Support III PS 30

Unnatural base pairs 54
Unnatural Base Pairs
5-Me-isodC  59
isodG 59

V

2’-F-U-ANA CE Phosphoramidite  1502'-OMe-5-Br-U-CE Phosphoramidite  146

178

Vitamin E 121

		INDEX
W
dW-CE Phosphoramidite 52

X
X

2’-dX-CE Phosphoramidite  65
7-deaza-dX-CE Phosphoramidite  63

X-ray crystallography 66

Y
Yakima Yellow®

Yakima Yellow® CPG  115Yakima Yellow® Phosphoramidite  114

ZZebularine

5-Me-2'-deoxyZebularine-CE Phosphoramidite  78
Zebularine-CE Phosphoramidite  140

Zip Nucleic Acid 54

Spermine Phosphoramidite 54

ZNA® 54MISCELLANEOUS

Spermine Phosphoramidite 54

179

GENERAL INFORMATIONORDERING
Orders may be placed by mail, telephone, fax or email to:
Glen Research Corporation
22825 Davis Drive, Sterling, VA 20164, USA(800) 327-GLEN(703) 437-6191(703) 435-9774 (Fax)orders@glenresearch.com
https://www.glenresearch.com
There is no minimum order requirement.  Our office hours are 9:30 a.m. to 5:30 p.m. EST,  Monday through Friday.  During
this time, Glen Research representatives will be available to take your order and answer any questions you may have regarding
our product line or DNA synthesis in general.  Messages may be left on voice mail at any other time.  Orders placed by 3:00
p.m. EST are normally shipped the same day.

DISCOUNTS
Glen Research offers a 10% discount on catalog products to educational institutions.  In addition, discounts based on volumeof usage are available, so please request a specific quotation.  We are also happy to quote on bulk quantities or custom
packaging of our products and on custom synthesis of unique materials.

TERMS AND CONDITIONS OF SALE
Delivery will be F.O.B. Glen Research, Sterling, VA.  Freight charges will be prepaid by Glen Research and will be included
on the invoice sent to the Customer.
Glen Research will issue an invoice to the Customer upon shipment of Products which shall be due and payable in full within
thirty (30) days of the date of the invoice. Amounts not paid when due may incur an interest charge of one and one-half  
(1-1/2) percent per month until fully paid. Customer shall be responsible for all taxes on Products sold to it, including stateand local sales and use taxes.  We reserve the right to require payment in advance before shipping any materials ordered.
Glen Research warrants that each product conforms to the specifications for such product. If the Customer notifies Glen
Research within thirty (30) days of its receipt of a product that the product does not conform to the specifications, Glen
Research will, at its option, replace the product or return the purchase price paid by Customer. No replacement or refund
will be made if the Customer does not notify Glen Research of a non-conforming product within said thirty (30) day period.
Glen Research makes no other express or implied warranty with respect to the products. Glen Research disclaims all implied
warranties, including the warranties of merchantability and fitness for a particular purpose. Glen Research’s liability forbreach of warranty is limited to refund of purchase price paid. In no event shall Glen Research be liable for lost profits, lossof goodwill or any incidental, special or consequential damages even if advised of the possibility of same.
It is the responsibility of the Buyer to determine the suitability of any of the listed products for any specific purpose.  
Responsibility for accidents arising from the handling and use of the listed products rests solely with the Buyer.  All of the
products should be handled only by trained personnel who are aware of the potential hazards and have ready access tosuitable safety equipment.  All products supplied are primarily for research and development purposes and Glen Research
products are not intended for use in foods or drugs, or for any commercial purpose.

PATENTSAs a research-oriented company, we realize the desirability of patents to cover original research and it is our policy to avoid
infringing any approved patents.  Accordingly, it is possible that some of our products may have to be withdrawn or adjusted
in price as patents are approved and issued.
©2021 Glen Research LLC

180

Oligo synthesis success. The first time and every time.

US Headquarters
Glen Research, LLC
22825 Davis Drive, Suite 100
Sterling, VA 20164
Phone: 703-437-6191
Fax: 703-435-9774

glenresearch.com© 2020 Glen Research. All rights reserved. For research use only.
Not intended for animal or human therapeutic or diagnostic use.