We are running Southern blots examining a DNA fragment of interest. We know the restriction sites and are using the appropriate RE’s at the correct concentrations.
However, one RE site that we know exists persistently fails to be cut with the RE’s.
This might suggest incomplete digestion?, methylation?, etc.
Has anyone encountered this problem? If so, do they have a solution?
Yes it might be methylation that is the cause. Unless there is another enzyme that is not affected by methylation that you can use you won’t be much you can do about this. Might be worth trying another enzyme site.
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