In-Gel Reactions

Section V: In-Gel Reactions

In This Section
Overview
Tips for Increasing the Efficiency of
In-Gel Reactions
Cloning in the Presence of Agarose
Restriction Digestion in the Presence of Agarose
DNA Amplification in the Presence of Agarose
References

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Section V: In-Gel Reactions
Overview

In-Gel Reactions

Introduction

Compatible agaroses

A variety of enzymatic reactions can be performed in thepresence of agarose. In-gel reactions are an alternative
approach to standard DNA recovery techniques andprovide a multitude of benefits. The use of in-gel reactions
will not only save time, but eliminate potential sample
loss during DNA recovery from an agarose gel.

In-gel reactions require the use of a low melting
temperature (65°C) agarose. Lonza has developed
two high quality Genetic Technology Grade™ (GTG®)
Agaroses for this application, specifically NuSieve®
GTG® and SeaPlaque® GTG® Agarose. These agaroses are
specifically designed and tested for compatibility with
in-gel reactions.

Advantages—— Avoids recovery losses—— NuSieve® GTG® Agarose is the choice for separation of
nucleic acids ≤1,000 bp with a resolving power of 4% 6% difference in DNA size—— Avoids recovery damage, especially shearing of higher
molecular weight DNA—— SeaPlaque® GTG® Agarose is the choice for separationof large nucleic acid fragments >1,000 bp

Applications
Enzymes active in the presence of low melting
temperature agaroses include:—— Alkaline phosphatase

The figures below demonstrate the efficiency of in-gel
cloning in our low melting temperature agaroses versus
sample recovery and also the consistency between
different agarose lots.
No.Transform antsperg ofVector—— Saves time otherwise used for recovery—— DNA polymerase I—— Klenow fragment—— Restriction endonucleases—— Reverse transcriptases

No. Transformants per g of Vector

Efficiency of In-Gel Cloning from SeaPlaque® GTG® Agarose—— BAL 31 nuclease

8.0x1077.0x1076.0x1075.0x1074.0x107—— T4 DNA ligase

3.0x107—— T4 DNA polymerase

2.0x107—— T4 polynucleotide kinase

1.0x1070—— T7 DNA ligase—— T7 DNA polymerase (Sequenase® Polymerase)—— Taq DNA polymerase

In-gelRecovered

Two lanes of Bst E II digest of lambda DNA were electrophoresed in a 1%
SeaPlaque® GTG® Agarose gel prepared in 1X TAE. The 2.3 kb band was
excised from each lane. One sample was ligated directly to pUC 19 in thepresence of remelted agarose (In-gel) and the other sample was purified
using a chaotrope-based recovery protocol (Recovered). Transformation
into DH5α® Cells was done following standard protocols.

A 377 bp fragment was electrophoresed inthree separate lots of a 3% NuSieve® GTG®
Agarose gel in 1X TAE Buffer then ligated to
M13 in the presence of remelted agarose.
Transformation into DH5αF′® Cells wasdone in remelted agarose following
standard protocols. Results 1, 2 and 3 arefrom three separate lots of NuSieve® GTG®
Agarose.

No. Transformants per g of Vector

Efficiency of In-Gel Cloning from NuSieve® GTG® Agarose
4.0x106

3.5x106

3.0x106

2.5x106

2.0x106

1.5x106

1.0x106

5.0x105

0

Lot 1

Lot 2

Lot 3

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Section V: In-Gel Reactions

Electrophoretic tips

Reaction tips—— Use a low EDTA (0.1 mM) 1X TAE Buffer;increases the availability of Mg+, a necessary cofactor
in many enzymatic reactions—— Melt the gel slice at 65°C - 70°C. Do not exceed 70°C as
this may cause melting of your DNA—— Briefly stain the gel after electrophoresis with GelStar®
or SYBR® Green I Nucleic Acid Gel Stain or ethidium
bromide; the presence of ethidium bromide during
electrophoresis can result in the degradation of DNA—— Visualize your DNA with a UV light source that is≥300 nm. Short UV wavelength light can damage
DNA; alternatively, DNA can be detected using Clare
Chemical’s Dark Reader® Transilluminator—— Minimize exposure of DNA to UV light to less than 1
minute—— The addition of 1 mM guanosine or cytidine to the gel
and electrophoresis buffer is effective in protecting
DNA against UV-induced damage; the nucleosides will
not impede electrophoresis, detection or purificationof DNA.
—— Limit the amount of DNA in the band of interestto 100 ng if possible; more DNA may cause
smearing and a wide band will result in an
unacceptably large piece of gel to be excised andmelted.
Effect of Agarose Concentration and Buffer on
In-Gel PCR200150—— Thoroughly mix the reaction components at 37°C 40°C this ensures proper mixing of DNA with reaction
components—— Do not exceed 0.5% SeaPlaque® GTG® or 1.5% NuSieve®
GTG® Agarose in the reaction mix—— Increase the efficiency of blunt end ligations; theaddition of larger amounts of vector, insert DNA and T4
DNA ligase or the addition of 5% (w/v) PEG-8000 to theligation mixture and incubating the ligation reaction
mixture for a longer time, can increase the efficiencyof the reaction; an alternative strategy is to add linkers
with sticky ends to the insert DNA—— When transforming cells, dilute the melted ligation
reaction mixture five-fold before adding to cells—— When transforming bacterial cells, dilute the agarose
containing the ligated DNA further with warmed(40°C) TAE or sterile distilled water before adding theligation reaction to the competent cells; it is betterto add 10 µl of a five-fold diluted mixture than 2 µlof a more concentrated reaction mixture; by doing
this, it is less likely that your ligated DNA will be
trapped in the agarose when it is added to the chilledcells; also be sure that you do not add excessive
DNA to the competent cells which can decrease thetransformation efficiency

H20
TAE
TBE

50

0.25

0.5
.05
0.75
Agarose Concentration in
Reaction Mixture (%)

1.0

1.25

1.5

A 500 bp PCR product was separated on 4% NuSieve® GTG® Agarose in either 1X
TAE or 1X TBE Buffer. Following electro­phoresis, the PCR product was reamplified
with the same primers as in the original amplification. Relative efficiency wasmeasured by comparing the products on an agarose gel.

No. of Recombinants
Per g Vector

Effect of UV Irradiation on In-Gel Cloning

100

0In-Gel Reactions

Tips for Increasing the Efficiency of In-Gel Reactions

Amount of Amplification
per % of Control

Returnto Main4.0x1073.0x1072.0x1071.0x1070

1

2
3
4
UV Exposure Time (Minutes)

5

A 2 kb fragment, separated in 1% SeaPlaque® GTG® Agarose and stained withethidium bromide, was exposed to 300 nm UV irradiation for different lengthsof time before excision from the gel, ligation into pBR322, and bacterial celltransformation. The mean of the number of white colonies per microgram vector
on two plates is given.

Reference
Gründemann, D. and Schömig, E., BioTechniques 21: 898 - 903, 1996.

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Section V: In-Gel Reactions
Cloning in the Presence of Agarose■■ Materials

In-Gel Reactions

Timetable
1.

(Day 1) Preparation of vector. Preparation of insert.
Preparation of competent cells.

2.

(Day 2) Ligation reaction. Transformation reaction.

3.

(Day 3) Assess the results obtained from the ligationtransformation reaction.

–– Sterile microcentrifuge (≥1 ml) and polypropylene
tubes (17 mm x 100 mm)–– Horizontal electrophoresis chamber–– Scalpel or razor blade–– Heating block or water bath–– Ice bucket and ice

Tips■■ Reagents—— Use 1X TAE Buffer with 0.1 mM EDTA.

–– SeaPlaque® GTG® or NuSieve® GTG® Agarose—— Electrophorese the DNA without ethidium bromide in
the gel.

–– GelStar® or SYBR® Green I Nucleic Acid Gel Stain or
ethidium bromide—— Minimize the exposure time of the DNA to less than 1
minute under UV light.

–– Distilled water—— Do not exceed a final concentration of 0.5% SeaPlaque®
GTG® or 1.5% NuSieve® GTG® Agarose in the reaction
mixture.

–– T4 DNA ligase–– Competent cells–– Restriction enzymes—— Dilute the agarose solution when running in-gel
transformations. Do not exceed >0.02% agarose in thetransformation reaction.

–– Calf intestine alkaline phosphatase

note: Electroporation can not be used with in-gel ligation/transformation procedures.

–– 10 mM Tris-HCl, pH 7.5–– 1X TAE (0.1 mM EDTA) Gel and Running Buffer–– Reagents for phenol extraction (Section VI)–– Ethanol–– 10X T4 ligation buffer

No. of Recombinants
Per g Vector

Effect of Agarose Concentration on Transformation

500 mM Tris-HCl, pH 7.5; 100 mM MgCl
50 mM Dithiothreitol; 10 mM ATP pH 7.6;
200.0 µg/µl nuclease-free BSA (bovine serum
albumin);4.0x1073.0x1072.0x1071.0x107
0

0.01

0.02
0.03
0.04
0.05
Agarose Concentration (%)

0.06

0.07

0.08

Caution: Materials and methods shown here present
hazards to the user and the environment. Refer tothe safety information on page 210 before beginningthese procedures.

Aliquots of agarose solutions (0.25%, 0.5%, 1.0% and 2.0% in 1X TAE)
were added to pUC19 monomer DNA which had been placed in labeled tubes.
Aliquots (6 µl=0.01 ng DNA) of the samples containing agarose were added
to 100 µl of (Invitrogen, Inc.) frozen competent cells on ice. The agarose
concentrations shown are those in the tubes of competent cells after samples
were added. Transformations were carried out following standard protocol.
Points shown on the graph represent the mean of three transformations.

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Section V: In-Gel Reactions
Cloning in the Presence of Agarose — continued

Preparing the vector

Ligation reaction

1.

Cut vector with appropriate restriction enzymes.

1.

2.

Dephosphorylate vector with calf intestine alkaline
phosphatase.

Remelt the agarose slice by heating to 68°C for 10
minutes.

2.

Place the remelted gel slice at 37°C until needed.

3.

Phenol extract vector.

3.

4.

Ethanol precipitate vector.

For a final reaction mixture of 50 µl, add the following
components in the following order:
Volume
18 µl
5 µl
1 µl

Preparing the insert
1.

Cut DNA to be used as insert with appropriate restriction
enzymes.

2.

Electrophorese DNA (100 ng) in a low melting
temperature agarose gel prepared in 1X TAE Buffer (0.1mM EDTA).

3.

Briefly stain DNA with GelStar® or SYBR® Green I Nucleic
Acid Gel Stain or ethidium bromide.

4.

Excise gel band containing insert and place in a sterile,
preweighed tube.

5.

Estimate the volume of the gel slice based upon theweight of the slice (e.g., 100 mg = 100 µl).

6.

Determine the concentration of the DNA in the gel sliceby assuming 100% recovery of DNA in the slice.

7.

Store excised band at 4°C until ready for use.

8.

Prepare agarose plates with the appropriate selective
media for the next day’s use.

1 µl

In-Gel Reactions

Returnto MainComponent
10 mM Tris-HCl, pH 7.5 or distilled H 0
10X T4 DNA ligation buffer
Vector (amount sufficient to obtain amolar ratio of insert to vector of 3 - 4:1)
T4 DNA ligase (between 1 - 2 units)
2

4.

Mix the components gently with a pipette.

5.

Add up to 25 µl of the remelted agarose gel slice [25 ng
of insert DNA]. Do not exceed a final concentration of
0.5% SeaPlaque® GTG® or 1.5% NuSieve® GTG® Agarosein the reaction mixture.

6.

Mix components by resuspending with a pipette.

7.

Ligate at room temperature for 2 - 3 hours.

Preparing competent cells
If you prepare your own competent cells, set up a small
overnight culture of cells. High transformation efficiencies
can be obtained with frozen competent cells that areeither prepared in the laboratory or purchased. Similartransformation efficiencies of 107 transformants/µg
pUC18 DNA with insert have been obtained using theHanahan Procedure (see citation at end of section);transformation efficiencies are reduced when using the
CaCl method.
2

note: Electroporation can NOT be used with in-gel
ligation/transformation procedures.

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Section V: In-Gel Reactions
Cloning in the Presence of Agarose — continued

In-Gel Reactions

Transformation reaction
The transformation procedure outlined below is a
modification of the Invitrogen procedure included with
their DH5α® Competent Cells. When using other frozen
competent cells follow manufacturer’s directions.
1.

Prepare competent cells if working with fresh cells. If
using frozen competent cells, remove cells from storage
and thaw on ice.

■■ Reagents–– SOC medium–– 	2.0 g Bacto-tryptone, 0.5 g Yeast extract, 1.0 ml 1 M
NaCl 0.25 ml 1 M KCl–– 	Dissolve in a final volume of 100 ml distilled water;
autoclave–– Add aseptically:–– 1.0 ml 2 M Mg2+
(1 M MgCl2, 1 M MgSO4, filter sterilized)

2.

Heat the ligation reaction at 68°C for 5 minutes to remelt
the agarose.

3.

Add competent cells into a prechilled polypropylene
tube (17 mm x 100 mm). We use 100 µl of thawed
DH5α® cells.

4.

Add 1 µl - 2 µl of diluted ligation reaction (70 pg - 140 pg
vector) to competent cells.

–– 10.0 g tryptone

Mix and incubate on ice for 30 minutes.

–– 10.0 g NaCl

5.

note: Exceeding 0.02% SeaPlaque® GTG® or NuSieve® GTG®
Agarose concentration in the final mixture may reducetransformation efficiencies.

–– 	1.0 ml 2 M glucose (filter sterilized)–– LB Agar Plates Supplemented with Ampicillin andX-gal (1 L)–– 5.0 g yeast extract–– 15.0 g agar–– 	800 ml distilled water–– 	Stir to dissolve components

6.

Heat shock the cells by placing the tubes in a 42°C
water bath for 45 seconds.

7.

Place the cells back on ice for 2 minutes.

–– 	Adjust volume to 1 L with distilled water8.

Add 0.9 ml of SOC medium to cells.

9.

Incubate at 37°C with shaking for 30 - 60 minutes.

–– 	Carefully heat while stirring until agar is
dissolved

10.

Spread 1 µl - 200 µl of the transformation mixture onto
an agar plate with the appropriate selective medium.

–– 	Remove stir bar and sterilize the medium by
autoclaving 25 minutes

11.

Allow the liquid to soak in.

12.

Invert the plates.

13.

Incubate overnight at 37°C.

–– 	Place the flask of medium in a water bath set
at 50°C and let the medium cool for at least 30
minutes–– 	Adjust to pH 7.5 with NaOH–– 	While medium is cooling, prepare ampicillin andX-gal stock solutions.
–– 	Add 1 ml of ampicillin stock and 2 ml of X-gal
stock to the tempered medium and pour into
plates–– 	Allow plates to sit on bench overnight to dry;then package and store at 4°C–– Ampicillin stock–– 	100.0 mg of ampicillin to 1 ml of sterile distilledwater–– X-gal (5-bromo-4-chloro-3-indoyl-ß-D-galactoside)stock–– 	40.0 mg of X-gal to 2 ml of dimethylformamide

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Section V: In-Gel Reactions
Cloning in the Presence of Agarose — continued

Controls

In-Gel Reactions

Returnto MainWe recommend the following controls be run in parallelwith the test plates:
VectorLigase# of blue# of white		colonies
colonies
pUC 18-native+++++
pUC18-singly digested+
efficiency
pUC18-singly digested+++++
pUC18-doubly digested+
background
pUC18-doubly digested++
				pUC18-native
+
+++++
-

Reason for control		
Cell competency test
Background for ligation efficiency
Determines ligation efficiency
Unrestricted vector background
Determines the efficiency of
double digestion
Reagent check

Assessing the results
Count colonies and assess the results of ligationtransformation. Colonies containing recombinant
plasmids should be white. Blue colonies result from
non-recombinant pUC18 plasmid.

References
Hanahan, D., J. Mol. Biol. 166: 557 - 580, 1983.
Crouse, G.F., et al., Meth. Enzymol. 1: 78 - 89, 1983.
Frischauf, A.M., et al., Nucl. Acids Res. 8: 5541 - 5549, 1980.
Majumdar, D., et al., BioTechniques 7: 188 - 191, 1989.
Murray, J.A.H., Nucl. Acids Res. 14: 10118, 1986.
Struhl, K., BioTechniques 3: 452 - 453, 1985.

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Section V: In-Gel Reactions
Restriction Digestion in the Presence of Agarose

In-Gel Reactions

Procedure ote: The urea sample buffer prevents the samples
nfrom regelling after digestion. It will also result in good
separation of the DNA during electrophoresis.
1.

Electrophorese DNA (several µg) in a low melting
temperature agarose prepared in 1X TAE Buffer (0.1mM EDTA).

2.

Briefly stain the gel with GelStar® or SYBR® Green I
Nucleic Acid Gel Stain or ethidium bromide.

3.

Excise the gel slice containing the DNA of interest andplace in a preweighed microcentrifuge tube.

4.

Estimate the volume of the gel slice based upon theweight and determine the concentration of the DNA
in the gel slice (e.g., 100 mg = 100 µl). Assume 100%
recovery of the DNA.

5.

Store excised band at 4°C until ready for use.

6.

Add sterile distilled water to bring volume of the gelslice to 200 µl (200 mg).

7.

Remelt the gel slice by heating to 68°C for 10 minutes.

8.

Mix the melted gel slice by pipetting.

9.

Remove a volume containing the quantity of DNA
needed for restriction digestion.

10.

Maintain the sample at 37°C to prevent gelling.

11.

Dilute the restriction endonuclease with the appropriate
reaction buffer.

12.

Digest DNA at the appropriate temperature and time foryour particular enzyme.

13.

Stop the reaction by adding 30 µl of urea sample buffer to
50 µl of the digestion mixture and mixing.

14.

Heat the sample to 65°C for 10 minutes if it hasregelled.

15.

Load the sample onto appropriate agarose gel for
analysis.

■■ Materials–– Horizontal electrophoresis chamber–– Scalpel or razor blade–– Microcentrifuge tubes (≥1 ml)–– Water bath or heating block■■ Reagents–– SeaPlaque® GTG® or NuSieve® GTG® Agarose–– 1X TAE (0.1 mM EDTA) Gel and Running Buffer–– Sterile distilled water–– GelStar® or SYBR® Green I Nucleic
Acid Gel Stain or ethidium bromide–– Restriction endonuclease(s)–– Urea sample buffer–– 	8% Ficoll® (Type 400) Polymer–– 27 mM EDTA	–– 0.27% bromophenol blue–– 5 M urea–– Adjust to pH 8.0
Caution: Materials and methods shown here present
hazards to the user and the environment. Refer tothe safety information on page 210 before beginningthese procedures.

References
Hermann, R.G. and Whitfeld, P.R., Methods in Chloroplast Molecular Biology,
Elsevier Biomedical Press, 1982.
Hermann, R.G., et al., Gene 8: 179 - 191, 1980.
Parker, R.C. and Seed, B., Meth. Enzymol. 65: 358 - 363, 1980.
Peacock, A.C., et al., Anal. Biochem. 149: 177 - 182, 1985.

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Section V: In-Gel Reactions
DNA Amplification in the Presence of Agarose

Procedure 1

Amplification Reaction Mixture
If the reaction buffer does not contain magnesium ion,
add sufficient amount for your template/primer.

1.

Electrophorese PCR products in low melting
temperature agarose prepared in 1X TAE (0.1 mM EDTA)
Buffer.

2.

Briefly stain the gel with GelStar® or SYBR® Green I Gel
Stain or ethidium bromide.

3.

Excise a gel slice containing the template DNA and place
into a preweighed microcentrifuge tube.

4.

Store the gel slice at 4° C protected from light until readyfor use.

5.

Melt the agarose gel slice containing template DNA at
65°C for 10 minutes.

6.

Dilute with 65°C, sterile distilled water to a final DNA
concentration of 0.1 ng/µl.

7.

Add a portion of the DNA into the amplification reaction
mixture (do not exceed 1 ng DNA/reaction).

8.

Combine the components of the reaction mixture.

9.

Vortex the reaction mixture to mix the contents.

–– Horizontal electrophoresis chamber

10.

Spin briefly in a microcentrifuge.

–– Scalpel or razor blade

11.

Overlay the mixture with mineral oil if necessary.

–– Vortex mixer

12.

Perform amplification reactions with conditions
appropriate for the template DNA and primers.

–– Microcentrifuge

13.

Remove mineral oil.

14.

Remelt the reaction mixture at 65°C prior to analyzing.

Procedure 2

Component
Volume (µl) FINAL		
Concentration
10X Reaction Buffer
5
1X
dNTP mix (1.25 mM each) 8
200 µM each
Primer #1, 10 µM
2.5
0.5 µM or 1.0 µM
Primer #2, 10 µM
2.5
0.5 µM or 1.0 µM
Template DNA + Agarose 5 - 10
(0.3 ng - 1.0 ng DNA)
Polymerase
0.5(2.5 units)
Sterile distilled water
to 50 µl■■ Materials–– Thin-walled microcentrifuge tube–– Microcentrifuge tubes (≥1 ml)–– Thermal cycler■■ Reagents–– SeaPlaque® GTG® or NuSieve® GTG® Agarose

1.

Follow steps 1 - 2 in Procedure 1.

–– 1X TAE (0.1 mM EDTA) Gel and Running Buffer2.

Turn the gel upside down while it is on the UVtransilluminator.

–– DNA amplification kit

3.

Stab the band of interest with a glass Pasteur pipette.
When the pipette is removed from the gel, a small plugof agarose will be contained in the tip.

–– Sterile distilled water

4.

Remove the plug of agarose.

5.

Add a portion of the plug of agarose to the amplification
reaction. The plug does not require melting; it will melt
during the first denaturing step.

6.

Follow steps 8 - 14 in Procedure 1.

In-Gel Reactions

Returnto Main–– Forward and reverse primers–– GelStar® or SYBR® Green I Nucleic
Acid Gel Stain or ethidium bromide
Caution: Materials and methods shown here present
hazards to the user and the environment. Refer tothe safety information on page 210 before beginningthese procedures.

References
Bjourson, A.J. and Cooper, J.E., Nucl. Acids Res. 20: 4675, 1992.
Fors, L., et al., Nucl. Acids Res. 18: 2793 - 2799, 1990.
Nichols, W.C., et al., Genomics 8: 318 - 323, 1990.
Wilkie, T.M. and Simon, M.I., Methods: A Companion to Methods in
Enzymology 2(1): 32 - 41, 1991.

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Section V: In-Gel Reactions
Restriction Digestion in the Presence of Agarose — continued

In-Gel Reactions
References for other in-gel reactions
Cycle Sequencing
Fraser, G.J., Resolutions 9(3): 1, 1993.
Gorman, K.B. and Steinberg, R.A., BioTechniques 7: 326 - 329, 1989.
Kretz, K.A. and O’Brein, J.S., Meth. Enzymol. 218: 72 - 79, 1993.
Random Prime Labeling
Daum, H.A. III, et al., BioTechniques. 11: 784 - 790, 1991.
Feinberg, A.P. and Vogelstein, B., Anal. Biochem. 137: 266 - 267, 1984.
Rose, E.A., et al., Cell. 60: 495 - 508, 1990.
Soreum, H., et al., App. Environ. Microbiol. 56: 1033 - 1037.
Blunt-end Ligation
Hemsley, A., et al., Nucl. Acids Res. 17: 6545 - 6551, 1989.
Majumdar, D., et al., BioTechniques 7: 188 - 191, 1989.
Murray, J.A.H., Nucl. Acids Res. 14: 10118, 1986.
Translation & Transcription of RNA
Brandt, T.L. and Hackett, P.B., Anal. Biochem. 135: 401 - 408, 1983.
Gallitelli, D. and Hull, R., J. Virol. Methods 11: 141 - 144, 1985.
Person, D.A. and Finn, O.J., BioTechniques 4: 398 - 399, 1986.
Attaching Linkers
Crouse, G.F., et al., Meth. Enzymol. 101: 78 - 89, 1983.
Gap Filling
Majumdar, D., et al., BioTechniques 7: 188 - 191, 1989.

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