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DNA Gel Cleanup Troubleshooting


DNA cleanup from gel is a powerful method to obtain highly pure DNA fragments, and gel purification kits are there to make it easier for you. At the same time, mistakes during gel extraction can potentially damage your DNA or result in low quality DNA fragments.

Low DNA Yield

  • Gel did not completely dissolve: Make sure that all the gel is completely dissolved before starting your reaction

  • Incomplete elution: If you are extracting a larger quantity of DNA, it might still be on the kit's column, or the input might be above the column's binding capacity. Perform multiple elution steps using the same column. Use fresh buffer per each elution.

Multiple Bands on Gel After Elution

  • Denaturation of DNA after elution: Long exposure to UV-light can degrade DNA. Minimize the exposure of your gel to UV when cutting your band of interest

  • Contaminated running chamber: Do not reuse running buffer or gel when running DNA for purification. Prepare fresh buffer and a new gel before each purification step

Low DNA Quality (Problems with Downstream Applications)

  • High salt content: Perform additional washing steps in your extraction

Next time you perform a DNA extraction from gel, make sure to follow these tips for a smooth gel extraction protocol

  • Use buffer and gel solution for your agarose gel preparation

  • Keep your agarose slice as small as possible

  • Split your agarose slice and run two purifications if you are planning of purifying a large amount of DNA

  • Minimize the exposure to UV light


Hopefully with these tips your problems will become a thing of the past. If you're still having issues - or have extra tips - let us or the community know in the comments!

Problems in the lab? Learn about methods and experiments in our Knowledge section or look up a specific Troubleshooting guide.