Oligo Handling, Analysis, and Applications
Support and Educational Content

Troubleshooting polyacrylamide gel electrophoresis (PAGE)

The IDT gel electrophoresis group runs preparatory polyacrylamide gels to purify certain oligonucleotides and can run up to 500 gels a day based on demand. Running that many gels means that this group has had a lot of experience with refining electrophoresis techniques and resolving gel issues. The following guide, provided by our gel electrophoresis team, contains troubleshooting tips for many of the gel issues they have come across during their work.


Troubleshooting guide

(Download a PDF of the following guide here.)


Click on your issue for possible solutions. 


Pouring problems

The gel leaks

The gel is not polymerizing or polymerizes too slowly

The gel sandwich separates

Setup problems

The buffer leaks when the gel is set up on the gel box

Running problems

There are no bubbles in buffer when running

The gel runs too fast/slow

The glass plates break during the gel run

Gel results problems

Gel bands do not migrate as expected

There is poor band resolution

"Smiling bands" are produced

The gel bands are streaked

There is no band


Performing PAGE is an art. It takes time and practice to familiarize yourself with the various gel box accessories, reagents, gel casting stand, and the electrophoresis unit. In addition, polyacrylamide gels are much thinner than agarose gels (typically <1 mm), making them prone to bubbles, and harder to handle. Pouring these gels definitely requires a certain finesse.

We hope this troubleshooting guide has addressed any PAGE issues experienced by your lab. Please contact our Technical Support group at applicationsupport@idtdna.com if you have further questions.

Authors: Kris Enequist and Kevin York are manager and assistant manager, respectively, of the IDT gel electrophoresis group.


Product focus—Oligonucleotides and primers, dsDNA fragments

Custom Oligonucleotides and primers

You can order up to 1 µmol desalted, custom synthesized DNA oligonucleotides and they will be shipped to you the next business day (larger scales are shipped within 5 business days). You can also specify whether to receive them dried down or hydrated, and whether you want them already annealed. Every IDT oligonucleotide you order is deprotected and desalted to remove small molecule impurities. Your oligos are quantified twice by UV spectrophotometry to provide an accurate measure of yield. Standard oligos are also assessed by mass spectrometry for quality you can count on.

Learn more or order now.


Custom dsDNA Fragments

Rather than annealing oligonucleotides to obtain dsDNA fragments, when your fragment size is 125 bp or longer, it might make more sense to order gBlocks® Gene Fragments. gBlocks Gene Fragments are double-stranded, sequence-verified, DNA genomic blocks, 125–2000 bp in length, that can be shipped in 2–5 working days for affordable and easy gene construction or modification. These dsDNA fragments have been used in a wide range of applications including CRISPR-mediated genome editing, antibody research, codon optimization, mutagenesis, and aptamer expression. They can also be used for generating qPCR standards.

Learn more about gBlocks Gene Fragments at www.idtdna.com/gblocks.

Additional reading

Running Agarose and Polyacrylamide Gels—Electrophoresis with agarose and polyacrylamide gels is one of the most widely used tools in molecular biology. Gels provide a simple, low-cost way to separate nucleic acids based on size for quantification and purification. Go over these tips for performing both types of electrophoresis.

Which Type of Purification Should I Choose?—Get these recommendations for oligonucleotide purification based on oligo length, application, yield required, and presence of modifications.

Designing PCR Primers and Probes—Review these general guidelines for designing primers and probes and for choosing target locations for PCR amplification.

© 2015, 2016 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see www.idtdna.com/trademarks.


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