MODified™ Protein
Domain Binding Kit

Catalog Nos. 13007(version A1)

Active Motif North America
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Copyright 2013 Active Motif, Inc.

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Information in this manual is subject to change without notice and does not constitute a commitment on the part of Active Motif, Inc. It is supplied on an “as is” basis without any warranty of any
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TABLE OF CONTENTS

Page

Overview  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Introduction . .  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
References  .  .  .  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Flow Chart of Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Kit Performance and Benefits  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  . 4MODified Histone Peptide Array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Kit Components and Storage .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  .  . 7Additional Materials Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Array Specifications  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Protocols
Buffer Preparation and Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Quick Chart for Preparing Buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  10
MODified Protein Domain Binding Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Section A. Protein Domain Binding Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Section B. Addition of Anti-His Antibody  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Section C. Addition of HRP-Conjugated Secondary Antibody  . . . . . . . . . . . . . . . . . . . . . . . 12
Section D. Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Section E. Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Appendix
Section F. Detection of Control Peptides  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  14
Section G. Troubleshooting Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Section H. Related Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Technical Services  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  18

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Overview
The epigenetic information that exists in the form of histone post-translational modifications(PTMs) on histone tails is generated, interpreted and edited by proteins that are coined ‘writers’‘readers’ and ‘erasers’. There are several classes of protein domains that influence gene regulationand chromatin remodeling by interacting with specific histone PTMs. Some common chromatin
remodeling protein domains include bromodomains, chromodomains and tudor domains to namea few.
The MODified™ Protein Domain Binding Kit is designed to be used in combination with Active
Motif’s MODified Histone Peptide Array* to screen His-tagged protein domains for interactions
with histones and their post-translational modifications. Each MODified array contains modifications to study histone acetylation, methylation, phosphorylation or citrullination on histones H2A,
H2B, H3 and H4. Each peptide is spotted in duplicate on the array to analyze the reproducibility ofthe binding events. This unique histone array contains up to four separate modifications per 19mer
peptide to allow researchers to study not only individual sites, but also the effects of neighboring
modifications on recognition and binding.
The MODified™ Protein Domain Binding Kit contains the buffers and reagents needed for analysisof His-tagged protein domain binding specificity towards histone PTMs and chemiluminescentdetection of the MODified Histone Peptide Arrays. The MODified Protein Domain Binding Kit
contains interaction buffer, wash buffer, anti-His6-tag antibody, HRP-conjugated secondary antibody and ECL reagents for chemiluminescent detection. For added convenience, a positive control
histone lysine methyltransferase G9a is included.
Following the interaction of the protein domain with the array and ECL detection, an image is thencaptured using a luminescent imaging system. Active Motif’s free Array Analyze Software can beused to analyze the intensity of the spots. Information about binding partners can be interrogatedthrough the software program to help identify the histone modifications associated with bindingof the protein domain.
The MODified Histone Peptide Arrays are available individually, or in packs of five. The arrays are
not included in the MODified Protein Domain Binding Kit and must be purchased separately.

product

formatcatalog no.

MODified™ Histone Peptide Array

1 array
5 arrays

13001
13005

MODified™ Protein Domain Binding Kit

5 rxns13007*CelluSpots™ arrays are manufactured under license by INTAVIS Bioanalytical Instruments AG

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1

Introduction
Epigenetic signals include DNA methylation, non-coding RNA, and post-translational modifications(PTMs) on the N-terminal histone tails. Histone modifications can consist of acetylation, mono-,di- (symmetric or asymmetric in the case of arginine) and tri-methylation of lysine and arginine
residues, phosphorylation of serine or threonine residues, citrullination and ubiquitination. Theseepigenetic marks play a role in the regulation of gene expression and chromatin state1-4.
These histone modifications are recognized and bound by specific proteins that are coined ‘writers’ ‘readers’ and ‘erasers’. Many of these proteins contain highly conserved domains which serveas the building blocks of the protein structure. Some of these domains have a clearly defined
function associated with them5-6. A multitude of protein domains exist, such as bromodomains,chromodomains and Tudor domains to name a few. Bromodomains are approximately 110 aminoacids folded into a left-handed four a-helical bundle. There are more than 70 identified membersof the bromodomain family. Bromodomains are known to bind acetylated lysine residues on histones or other proteins. They regulate chromatin structure and gene expression as part of histone
acetyltransferases or chromatin remodeling factors. Please visit www.activemotif.com for a list of
bromodomain proteins available from Active Motif.
The Tudor domain folds into a b-sandwich flaked by one a-helix. Tudor domains are known tobind methylated lysine or arginine residues on Histone H3 and H4 and are believed to be involved
in RNA binding, DNA damage response and chromatin modifications. Chromodomain proteins bindto methylated lysines on Histone H3 and are associated with the assembly of protein complexes
that modify chromatin into condensed heterochromatin, such as transcriptional repressors HP-1,
Polycomb (Pc) and the human retinoblastoma binding protein (RBP-1).
Our current understanding of these protein domains has been limited by the lack of appropriate
tools to fully interrogate their binding specificity. Active Motif’s MODified Histone Peptide Array
and its associated MODified Protein Domain Binding Kit provide a solution to this problem. The
array contains 59 post-translational modifications in different combinations to allow researchers to screen a large panel of histone modifications in a single experiment. The results provide
information on protein domain interactions with specific histone modifications and also reveals
the influence that adjacent modifications may play on protein binding.

References
1.
2.
3.
4.
5.
6.

Kouzarides T. (2007) Cell, 128 (4): 693-705.
Lee J.S. et al. (2010) Cell, 142 (5): 682-685.
Berger. S.L. et al. (2007) Nature, 447 (7143): 407-412.
Sims, R.J. and Reinberg, D. (2008) Nat Rev Mol. Cell Biol, 9 (10): 815-820.
Jenuwein, T. and Allis, C.D. (2001) Science, 293 (5532): 1074-1080.
Yun, M. et al. (2011) Cell Res, 21 (4): 564-578.

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2

Flow chart of process
Blocked slide
Blocking
MODified™ Histone Peptide Array
Wash
Incubation with:
His-tagged protein domain
Wash

Data analysis with:
Array Analyze software

Incubation with:
Anti-His-tag antibody

Wash
Detection by:
Chemiluminescence

Wash

Incubation with:
HRP-conjugatedsecondary antibody

Flow Chart of MODified Protein Domain Binding Kit.
The MODified Histone Peptide Array is used in combination with the MODified Histone Protein Domain Binding Kit. The
simple assay works like a Western blot. The array is incubated in blocking buffer. Then, the His-tagged protein domain
of interest is added to the array followed by detection via an anti-His6-tag antibody and an HRP-conjugated secondary
antibody. ECL detection is used to produce a chemiluminescent signal that is captured using a CCD camera or film. The
array image is then analyzed using the Array Analyze software program to determine the spot intensity and identify protein
domain binding partners.

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3Kit Performance and Benefits
The MODified Histone Peptide Array can be used to screen antibodies, proteins and enzymes forinteractions with histones and their post-translational modifications.
The array contains 59 different post-translational modifications for histone acetylation, methylation, phosphorylation and citrullination modifications on the N-terminal tails of histones H2A,
H2B, H3 and H4. Each 19mer peptide may contain up to four modifications each. Five control spots
are included on each array (locations P20-P24): biotin peptide, c-Myc tag, no histone peptide andtwo background spots containing a mixture of modifications that are present on the array.
The MODified Protein Domain BInding Kit includes Recombinant His-tagged G9a, a known histone
methyltransferase that targets lysine 9 on Histone H3, as a positive control protein.

MODified Histone Peptide Array

MODified Histone Peptide Array and reference grid for histone peptide locations.
Histone peptides containing 384 different modification combinations are spotted in duplicate onto the glass slide. One
spot is located on the left side of the slide and the duplicate spot is on the right side of the slide. The reference Excel filewith the corresponding histone peptide content can be downloaded from Active Motif’s website at www.activemotif.
com/modified.

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4

Example Analysis of Bromodomain BRD4 Protein Domain (333-460)

Image of ECL detection of Bromodomain-containing protein 4 (BRD4).
Recombinant His-tagged BRD4 (333-460) protein domain (Active Motif Catalog No. 31446) was incubated with the MODified Histone Peptide array in combination with a c-Myc antibody (Active Motif Catalog No. 39502) for control peptide P21
according to the MODified Histone Protein Domain Binding manual at a concentration of 180 nM for 2 hours. The antiHis6-tag antibody and c-Myc antibody were each used at a 1:6,000 dilution, followed by incubation with the anti-mouse
HRP-conjugated antibody at a 1:2,500 dilution and ECL detection. The chemiluminescent signal from the array was captured
with a CCD camera. The image shows the grid overlay from the Array Analyze software for spot identification on the left
hand side of the array image.

BRD4 Specificity Factor (Multiple Peptide Average)
16

Specificity Factor

14
12
10
8
6
4
2
0

c
36a

K
H3

H4

ac

K8

c
12a

K
H4

ac

20

K
H4

H4

ac

K5

e3

36m

K
H3

e2

e1

36m

K
H3

36m

K
H3

H4

ac

K16

e2a

3m

R
H4

Modification
Graphical analysis of the BRD4 protein domain.
Active Motif’s Array Analyze Software was used to analyze spot intensity from the chemiluminescent image. The results
were graphed as a specificity factor, which is the ratio of the average intensity of all spots containing the modification
divided by the average intensity of all spots not containing the modification. The graph shows the top ten most reactive
histone modifications based on the specificity factor values. The binding of BRD4 protein domain (333-460) showed specificity towards binding of acetylated histone lysine residues, confirming the usefulness of the MODified Peptide Array as atool to screen for protein domain binding specificity.

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5

Example Analysis of Positive Control G9a protein

Image of ECL detection of positive control Recombinant His-G9a protein.
The positive control His-G9a protein was incubated with the MODified Histone Peptide array in combination with a c-Myc
antibody (Active Motif Catalog No. 39502) for control peptide P21 according to the MODified Histone Protein Domain
Binding manual at a concentration of 10 nM for 2 hours. The anti-His6-tag antibody and c-Myc antibody were each used
at a 1:6,000 dilution, followed by incubation with the anti-mouse HRP-conjugated antibody at a 1:2,500 dilution and ECL
detection. The chemiluminescent signal from the array was captured with a CCD camera. The image shows the grid overlay
from the Array Analyze software for spot identification on the left hand side of the array image.

G9a Specificity Analysis (Multiple Peptide Average)
12

Specificity Factor

10
8
6
4
2
0

e2

9m

K
H3

e1

2s

me

9m

K
H3

H

8
3R

2a

me

H

8
3R

2a

2s

me

me

2
3R

2
3R

H

H

H3

ac

K4

e3

4m

K
H3

e2

4m

K
H3

e1

4m

K
H3

Modification
Graphical analysis of the positive control G9a protein.
Active Motif’s Array Analyze Software was used to analyze spot intensity from the chemiluminescent image. The results
were graphed as a specificity factor, which is the ratio of the average intensity of all spots containing the modification
divided by the average intensity of all spots not containing the modification. The graph shows the top ten most reactive
histone modifications based on the specificity factor values. G9a is a known histone methyltransferase associated with thespecific mono- and di-methylation of lysine 9 on Histone H3. The data shown here confirm the association of G9a with its
preferred histone modifications.

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6

Kit Components and Storage
MODified Histone Peptide Arrays and the MODified Protein Domain Binding Kit are for researchuse only. Not for use in diagnostic procedures. All components are guaranteed stable for 6 months
from date of receipt when stored properly.
Reagents

Quantity

Storage

10X Wash Buffer AM4

100 ml4°C

Anti-mouse HRP-conjugated secondary antibody

10 µl

4°C

ECL Reagent A

50 µl

4°C

ECL Reagent B

2 x 13 ml

4°C

Blocking Buffer AM2

100 ml-20°C

Interaction Buffer AM1

50 ml

-20°C

1 M DTT

100 µl-20°C

Anti-His6-tag antibody

10 µl

-20°C

Recombinant His-G9a

20 µl

-80°C

Additional materials required but not provided• MODified Histone Peptide Arrays• His-tagged protein domain of interest• Luminescent imaging system with CCD camera or X-ray film
• NUNC Well Rectangular Dishes (Catalog No. 267061) or suitable chamber for array incubation• Active Motif’s free Array Analyze Software program capable of analyzing MODified Histone
Peptide Arrays (available for download at www.activemotif.com/modified)
Array specifications (not included in the MODified Protein Domain Binding Kit)
• Standard microscope slides (26x76 mm, white coating)• 768 spots per slide (384 peptide-conjugate spots printed in duplicate)• Spot-to-spot distance 1.2 mm• Peptides are covalently bound to cellulose via C-terminus• Arrays contain control peptides and location marks

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7

Protocols
Buffer Preparation and Recommendations
Blocking Buffer AM2
Thaw the blocking buffer prior to starting the assay. Once thawed, the buffer should be stored at
4°C and used within 24 hours. Otherwise, the buffer should be re-frozen at -20°C.
Interaction Buffer AM1
Thaw the Interaction Buffer AM1 prior to starting the assay. Once thawed, the buffer should be
stored at 4°C and used within one week. Otherwise, the buffer should be re-frozen at -20°C. Eacharray will need 10 ml of complete Interaction Buffer, which should be prepared fresh for eachexperiment by adding 1 µl of 1 M DTT to 10 ml Interaction Buffer AM1.
Preparation of 1 X Wash Buffer
Prepare the amount of 1X Wash Buffer required for the labeling assay as follows: For every 100 ml
of 1X Wash Buffer required, dilute 10 ml 10X Wash Buffer AM4 with 90 ml distilled water (see the
Quick Chart for Preparing Buffers). Mix gently to avoid foaming. The 1X Wash Buffer may be stored
at 4°C for one week. The Tween 20 contained in the 10X Wash Buffer AM4 may form clumps,
therefore it is necessary to completely resuspend any precipitates by incubating at 50°C for 2
minutes and mixing prior to use.
Sample Protein Domains
Transfer 5 ml of the complete Interaction Buffer containing DTT (prepared above) to a 15 ml conical tube. Dilute the His-tagged protein domain of interest in the Interaction Buffer. We recommend a range of 10 nM - 1 µM as a starting concentration. You may need to perform a titration of
the protein domain to determine an optimal concentration for binding.
Note:

The MODified Protein Domain Binding Kit is designed for use with His-tagged
protein domains. If working with a GST or FLAG-tagged protein, please contact
Active Motif’s Technical Support team at tech_service@activemotif.com forrecommendations on appropriate antibodies to use for detection.

Anti-His6-tag Antibody
This antibody is used to detect the His-tag on the protein domain of interest. Dilute the AntiHis6-tag antibody 1:3,000 in 1X Wash Buffer by adding 2 µl of antibody to 6 ml 1X Wash Buffer.
Anti-mouse HRP-conjugated secondary antibody
The anti-mouse HRP-conjugated secondary antibody should be diluted 1:2,500 by adding 2 µl of
HRP-conjugated antibody to 5 ml 1X Wash Buffer.
Detecting Solution
To prepare the Detecting Solution, dilute ECL Reagent A into ECL Reagent B in a 15 ml conicaltube. For a single array, add 1.5 µl of ECL Reagent A to 5 ml of ECL Reagent B. Vortex briefly tomix. Detecting Solution should be prepared just before use and kept protected from light. The
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8Detecting Solution should be added drop wise onto the array while gently tilting the array toensure complete coverage of Detecting Solution over the full array (complete coverage may only
require approximately 750 µl of Detecting Solution). The array needs to remain wet during image
capture. We recommend covering the array with clear plastic wrap or an acetate sheet during image capture to maintain the moisture.
Note:

The MODified Histone Peptide Arrays have been validated for use on the LICOR® Odyssey Infrared Imaging System. To adapt the protocol for use with theinfrared system, the appropriate infrared fluorescence secondary antibody andimaging system would be required in place of the anti-mouse HRP-conjugatedsecondary antibody and detecting solution.

Positive Control Recombinant His-G9a (Optional)
Recombinant His-G9a protein is provided as a positive control for the MODified Protein Domain
Binding Kit. G9a is a histone lysine methyltransferase that specifically targets lysine 9 on Histone
H3 for mono- and dimethylation. Due to the number of peptides containing Histone H3 lysine 9
on the array, it is not recommended to combine this positive control protein with your protein
domain of interest. The Recombinant His-G9a protein is provided as an optional control that canbe used to confirm the activity of your assay reagents, but should be tested on a separate MODified Histone Peptide Array than your protein of interest. Enough protein is supplied to run a single
positive control experiment. The Recombinant His-G9a is provided ready to use. Add 20 µl G9a
protein to 5 ml complete Interaction Buffer and add to a separate array.
Note:

See the Control Peptides section below and Appendix Section F for details
regarding the use of a positive control antibody in combination with the sample
protein domain of interest on the same array.

Control Peptides
The MODified Histone Peptide Array contains control spots (locations P20-P24), as referenced on
the Excel file (www.activemotif.com/modified). The control c-Myc tag can be detected with ananti-c-Myc antibody (Catalog No. 39502). The control biotin peptide can be detected with either
an anti-biotin antibody or a streptavidin-conjugated antibody. The array also contains a nohistone negative control peptide and two spots for background levels. Control antibodies can be
combined with the anti-His6-tag antibody for dual detection on the same array, as described inAppendix Section F: Detection of Control Peptides.

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9Quick Chart for Preparing Buffers
Reagents to prepare

Components

1 array

5 arrays

Blocking Buffer AM2

TOTAL REQUIRED

5 ml

25 ml

Interaction BufferInteraction Buffer AM1
1 M DTTTOTAL REQUIRED

10 ml
1 µl
10 ml

50 ml
5 µl
50 ml

1X Wash Buffer

10X Wash Buffer AM4
Distilled water
TOTAL REQUIRED

10 ml
90 ml
100 ml50 ml
450 ml500 mlECL Reagent A

TOTAL REQUIRED

1.5 µl7.5 µlECL Reagent B

TOTAL REQUIRED

5 ml

25 ml

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10

Array Protocol
Read the entire protocol before use.
MODified Protein Domain Binding Kit Protocol
The protocol below is for screening protein domain interactions with histones and histone modifications using a chemiluminescent detection method. Prepare the Interaction Buffer, Blocking
Buffer and 1X Wash Buffer as described above in the section Buffer Preparation and Recommendations. The protocol below is for the analysis of a single array. If screening multiple arrays at thesame time, use the Quick Chart for Preparing Buffers to determine the total volumes needed.
It is very important to ensure that the entire surface of the MODified Histone Peptide Arrays arecompletely covered with liquid during all incubation and wash steps. Uneven distribution of liquid
will result in inconsistent results. Do not touch or handle the membrane portion of the MODified
Histone Peptide Array. Handle the array by the edges of the slide only.

Section A: Protein Domain Binding Interactions
1.

Transfer 10 ml of thawed Blocking Buffer AM2 into 15 ml conical tube. Blocking Buffer AM2
can be kept at 4°C for up to 24 hours.

2.

Immerse one array in 5 ml Blocking Buffer AM2.
Note:

If working with multiple arrays at the same time, “4 Well Rectangular Dishes”
from NUNC (Catalog No. 267061) can be used for the incubation and wash steps.
The NUNC dish does not contain a lid, so it is recommended to use a low setting
on an orbital shaker when performing incubation and wash steps. Other suitablecontainers may also be used.

3.

Incubate on an orbital shaker for 1-4 hour(s) at room temperature, or overnight at 4°C.

4.

Carefully pour off the buffer. Perform a quick rinse (30 seconds) with 5 ml 1X Wash Buffer.
Then wash two times for 5 minutes each on an orbital shaker using 5 ml 1X Wash Buffer.

5.

During the last wash step, prepare 10 ml of Interaction Buffer according to the Buffer Preparation and Recommendation Section on page 8.

6.

Wash the array one time with 5 ml Interaction Buffer using an orbital shaker for 5 minutes atroom temperature.

7.

Add the His-tagged protein domain being studied and any necessary co-factors to 5 ml ofInteraction Buffer. We recommend testing your protein domain in the range of 10 nM to1 µM. Incubate the protein domain with the blocked array for 2 hours at room temperature. Set the orbital shaker to a low setting to prevent any cross contamination of protein
domains if working with more than one array.
Note:

If using the positive control His-G9a on the array, add 20 µl protein (10 nM final
concentration) to 5 ml Interaction Buffer.

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11Section B: Addition of Anti-His Antibody
1.

Perform a quick rinse (30 seconds) with 5 ml 1X Wash Buffer. Then wash three times for 5
minutes each on an orbital shaker using 5 ml 1X Wash Buffer.

2.

During the last wash step, prepare the anti-His antibody dilution. Dilute the anti-His antibody 1:3,000 by adding 2 µl anti-His tag antibody to 6 ml 1X Wash Buffer.

3.

Add the 6 ml anti-His tag antibody to the array and incubate for 1 hour at room temperature
on an orbital shaker.

Section C: Addition of HRP-Conjugated Secondary Antibody
1.

Perform a quick rinse (30 seconds) with 5 ml 1X Wash Buffer. Then wash three times for 5
minutes each on an orbital shaker using 5 ml 1X Wash Buffer.

2.

During the last wash step, prepare the secondary antibody dilution. Dilute the anti-mouse
HRP-conjugated antibody 1:2,500 by adding 2 µl anti-mouse HRP to 5 ml 1X Wash Buffer.

3.

Add the 5 ml anti-mouse HRP-conjugated secondary antibody dilution to the array andincubate for 1 hour at room temperature on an orbital shaker.

4.

Perform a quick rinse (30 seconds) with 5 ml 1X Wash Buffer. Then wash three times for 5
minutes each on an orbital shaker using 5 ml 1X Wash Buffer.

5.

During the last wash step, prepare the Detecting Solution as stated in the Buffer Preparation
and Recommendations section on page 8.

Section D: Detection
1.

The Detecting Solution should be added drop wise onto the array while gently tilting thearray to ensure complete coverage (approximately 750 µl of Detection Solution is required
to completely cover the array). Let sit for 5 minutes at room temperature. The array needs toremain wet during image capture. We recommend covering the array with clear plastic wrap
or an acetate sheet during image capture to maintain the moisture.
Note:

2.

If working with multiple arrays at the same time, we recommend going throughthe entire detection process and image capture with a single array and thenmoving on to the second array and so forth. Additional arrays can remain in the
final wash from the secondary antibody until they are ready to be processed.

Use a CCD camera, or film, to capture images at multiple exposure times (e.g. 10 sec., 30 sec.,
1 min., 2.5 min., 5 min. and 10 minutes). For weak protein domain binding interactions, an
exposure of 10-15 minutes may be needed for sufficient detection. It is also recommended
to take a white light image of the array in order to obtain orientation information for the
analysis step.

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12Section E: Analysis
1.

Save the image file as a .tif file and compare the image to the reference grid containing thehistone peptide content. The .tif file will need to be resized to approximately 3298 pixels
wide by 1161 pixels high for use in Active Motif’s Array Analyze Software. Select constrain
proportions to keep the scale consistent when resizing. (With constrain proportions selected
only one value, either the width or height needs to be changed. The other value will auto
correct.) Programs such as Adobe Photoshop or the freeware program, GIMP2 (http://www.
gimp.org/) will allow you to open and resize .tif files. The image should also be saved with amode value of 8 Bits/Channel.
The reference Excel file for the histone peptide content and associated grid location can be
downloaded from our website at www.activemotif.com/modified.

2.

Active Motif’s free Array Analyze software is available for analysis of the MODified Histone
Peptide Arrays. The software program will analyze the spot intensity of the interactions fromthe array and generate a graphical analysis of the histone peptide interactions. Information
about spot intensity, averages and errors can be saved in Excel-compatible files to allow
for individual analysis. The Array Analyze software is designed for use on PCs only. Please
download the Array Analyze manual for information about the installation and operation of
the program. Both the manual and the Array Analyze Software can be downloaded from our
website at www.activemotif.com/modified.

3.

(Optional) Use a spot densitometry program to determine the relative intensity of each peptide. Compare the image file to the reference grid containing the histone peptide content.

www.activemotif.com

13

Appendix
Section F: Detection of Control Peptides
This protocol is designed for researchers that want to include an antibody for detection of one of
the control peptides (c-Myc or biotin) in combination with detection of their His-tagged protein
domain of interest. We recommend detection of the c-Myc control spot (P21) using Active Motif’s
c-Myc antibody (Catalog No. 39502), as it can be used in combination with the supplied antimouse HRP-conjugated secondary antibody. If using another c-Myc antibody or an antibody todetect the biotin control peptide, it is necessary to use an antibody raised in mouse in order toutilize the anti-mouse HRP-conjugated secondary antibody for detection.
1.

Dilute the antibody for the control peptide of interest (c-Myc or biotin) according to theWestern blot dilution recommendations of the antibody supplier (For Cat# 39502, c-Myc antibody, we recommend using a 1:6,000 dilution). The antibody dilutions should be made into
the same 6 ml 1X Wash Buffer used for the anti-His antibody such that the two antibodies
are combined for simultaneous incubation (Section B, Step 2).

2.

Add the 6 ml of combined anti-His and control spot antibody dilutions to the array andincubate for 1 hour at room temperature on an orbital shaker. Set the orbital shaker to a low
setting to prevent any cross contamination of antibody solutions if working with more than
one array.

3.

Proceed to Section C: Addition of HRP-conjugated secondary antibody and continue with
the instructions in the protocol.

www.activemotif.com

14Section G: Troubleshooting Guide
Problem/question

Possible cause

Recommendation

No signal or weak signal

Omission of key
reagent

Check that all reagents have been added to the array in thecorrect order.

Substrate is no longer
activeTest conjugate and substrate for activity by mixing a small
amount of HRP and detecting solution together.

Enzyme inhibitor
present

Sodium azide will inhibit peroxidase reactions (HRP-conjugates). Follow our recommendations to prepare buffers.

Concentration ofprotein domain is
too low

Titrate the amount of protein domain to use in the assay for
optimal binding. We recommend a range of 10 nM to 1 µM.

CCD camera settings
not optimal

Verify the filter settings on the CCD camera and make surethey are set to detect luminescence

Concentration ofprotein domain is
too high

Titrate the amount of protein domain to use in the assay for
optimal binding. We recommend a range of 10 nM to 1 µM.

Non-specific protein
binding

Some protein domain do not have specific histone binding
partners. As a result, the protein may bind to a large numberof peptides on the MODified Histone Peptide Array. This may
appear as background signal due to the highly promiscuous nature of the protein domains. Confirm with publishedliterature the expected histone binding sites for your protein
domain of interest.

Not enough solution
used for incubation
and wash steps

It is very important to ensure that the entire surface of the
MODified Histone Peptide Arrays are completely covered withliquid during all incubation and wash steps. Uneven distribution of liquid will result in inconsistent results. If using large
containers for incubation and wash steps it may be necessary
to increase the volume of solution used.

Incubation steps performed on an unevensurface

It is very important to ensure that the entire surface of the
MODified Histone Peptide Arrays are completely covered withliquid during all incubation and wash steps. Uneven distributionof liquid will result in inconsistent results. Ensure that the arrayis placed on a flat, level surface during all incubation and wash
steps.

Array dried out during
image capture

During long exposure times it is possible for the Detection
Solution to be completely absorbed by the array, causing
the array to dry out. Place a sheet of clear plastic wrap or an
acetate sheet over the array in order to keep the array wet
during image capture.

High background

Uneven detection orinconsistent replicates

Can the MODified Histone
Peptide Arrays be stripped
and re-used?

www.activemotif.com

No. The MODified Histone Peptide arrays are suitable for one
use only. Standard stripping procedures do not adequately
remove the existing bound antibody and harsh conditions cancleave the peptide bond to the array.

15

Problem/question

Possible cause

Recommendation

What if my protein
domain of interest
contains a GST or FLAG tag
instead of a His tag?

The MODified Protein Domain Binding Kit is designed to be
used with His-tagged proteins and therefore includes an antiHis-tag antibody for detection. To modify the assay for use
with a protein containing a GST, FLAG or other tag you would
need to identify a suitable tag specific antibody for substitution in the kit and an associated HRP-conjugated secondary
antibody. Please contact our technical support department forrecommendations on appropriate antibodies to use for thisapplication.

What are the chemical
stability limits of thearrays?

The arrays are stable at the physiological pH values. They aresensitive to mechanical stress and should not be touched or
wiped. Furthermore, the arrays should not be treated withstrong acids and bases, since the peptide bond and/or thelinker between the peptide and cellulose can be cleaved. The
treatment with organic solvents like ethanol should also be
avoided. Several salt concentrations have been tested forblocking and wash buffers, and the arrays are robust in thisrespect.

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16Section H. Related Products
Histone ELISAs		FormatCatalog No.

Histone H3 monomethyl Lys4 ELISA		Histone H3 dimethyl Lys4 ELISA		Histone H3 trimethyl Lys4 ELISA		Histone H3 dimethyl Lys9 ELISA		Histone H3 trimethyl Lys9 ELISA		Histone H3 monomethyl Lys27 ELISA		Histone H3 trimethyl Lys27 ELISA		Histone H3 phospho Ser10 ELISA		Histone H3 phospho Ser28 ELISA		
Total Histone H3 ELISA		

1 x 96 rxns
1 x 96 rxns
1 x 96 rxns
1 x 96 rxns
1 x 96 rxns
1 x 96 rxns
1 x 96 rxns
1 x 96 rxns
1 x 96 rxns
1 x 96 rxns

53101
53112
53113
53108
53109
53104
53106
53111
53100
53110

Recombinant Histones		

FormatCatalog No.

Recombinant Histone H2A		
Recombinant Histone H2B		
Recombinant Histone H3 (C110A)		
Recombinant Histone H3 biotinylated		
Recombinant Histone H3K4me1		
Recombinant Histone H3K4me2		
Recombinant Histone H3K4me3		
Recombinant Histone H3R8me2a		
Recombinant Histone H3 monomethyl Lys9		
Recombinant Histone H3 dimethyl Lys9		
Recombinant Histone H3 trimethyl Lys9		
Recombinant Histone H3 monomethyl Lys27		
Recombinant Histone H3 dimethyl Lys27		
Recombinant Histone H3 trimethyl Lys27		
Recombinant Histone H3 monomethyl Lys36		
Recombinant Histone H3 dimethyl Lys36		
Recombinant Histone H3 trimethyl Lys36		
Recombinant Histone H3 monomethyl Lys79		
Recombinant Histone H3 dimethyl Lys79		
Recombinant Histone H3 trimethyl Lys79		
Recombinant Histone H4		
Recombinant Histone H4 monomethyl Lys20		
Recombinant Histone H4 dimethyl Lys20		
Recombinant Histone H4 trimethyl Lys20		

50 µg
50 µg
100 µg
25 µg
50 µg
50 µg
50 µg
25 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg
50 µg

31251
31252
31207
31271
31208
31209
31210
31276
31211
31212
31213
31214
31215
31216
31217
31218
31219
31220
31221
31222
31223
31224
31225
31226

Active Motif also offers a growing list of application validated antibodies, including antibodies
for histones and histone modifications, transcription factor antibodies, DNA methylation-related
antibodies and ChIP validated antibodies. For a complete list go to www.activemotif.com/abs

www.activemotif.com

17Technical Services
If you need assistance at any time, please call Active Motif Technical Service at one of thenumbers listed below.
Active Motif North America
1914 Palomar Oaks Way, Suite 150
Carlsbad, CA 92008
USA
Toll Free:877 222 9543
Telephone: 760 431 1263
Fax:
760 431 1351
E-mail:tech_service@activemotif.com
Active Motif Europe
104 Avenue Franklin Roosevelt
B-1330 Rixensart, Belgium
UK Free Phone:		
0800 169 31 47
France Free Phone:
0800 90 99 79
Germany Free Phone: 0800 181 99 10
Telephone: 		+32 (0)2 653 0001
Fax: 		
+32 (0)2 653 0050
E-mail: 		
eurotech@activemotif.com
Active Motif Japan
Azuma Bldg, 7th Floor
2-21 Ageba-Cho, Shinjuku-Ku
Tokyo, 162-0824, Japan
Telephone: +81 3 5225 3638
Fax:
+81 3 5261 8733
E-mail:japantech@activemotif.com
Visit Active Motif on the worldwide web at http://www.activemotif.com
At this site:• Read about who we are, where we are, and what we do• Review data supporting our products and the latest updates• Enter your name into our mailing list to receive our catalog, MotifVations newsletter andnotification of our upcoming products• Share your ideas and results with us• View our job opportunities
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18