electrophoresis of PCR products

Squid besco.1 at osu.edu
Fri Sep 8 14:28:18 EST 2000

I am trying to clearly separate two DNA bands on a gel.  The difference
between them is 27 bp, and the overall size is between 100 - 200 bp.  I have
tried 5% acrylamide gels, and get very sharp defined bands, but my negative
control lane always looks lousy.  The same tube run on a 2% agarose gel
looks much better (ie negative control lane empty) but there is not a clear
separation of my two bands of interest.
Any suggestions for what kind of gel I should be running?
Or what I am doing wrong with the acrylamide?

many thanks


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