Restriction Enzyme Digestion Problem: DNA Smear on Agarose Gel

Learn more about what causes this common problem, and how NEB's enzymes are QC'd to avoid DNA smearing.


Jenna Ware:
A commonly asked question is, "Why am I seeing a DNA smear on my agarose gel?" One possible reason for this is that you have nuclease contamination. Our restriction enzymes are tested for nuclease contamination so it could be other components in your reaction that are causing this problem, such as the DNA, the buffer, or the water.

Another reason you might see this is because your running buffer in your gel box could be causing this. Another possibility is that you might be using a restriction enzyme that has high binding affinity to your DNA. Some enzymes have a higher binding affinity to DNA than others.

To avoid this problem you could add a 0.1% to 0.5% SDS solution and that will help the enzyme dissociate from the DNA.

Those are some of the reasons that you might see a DNA smear on your agarose gel. If you have any other problems or still troubleshooting you can look at our website, on our troubleshooting guide to help you, or feel free to call us and we can help.

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