electrophoresis of PCR products

Chunxin Wang cxwang at wam.umd.edu
Fri Sep 8 15:11:54 EST 2000

try 3-4% agarose gel. Usually 4% gel can ensure separation of 10%
difference of the size. Sometimes, 3% gel is ok if the overall size is
around 100 bp.


On Fri, 8 Sep 2000, Squid wrote:

> 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
> Julie


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