electrophoresis of PCR products

[Mr JN Goulding]

You could try using a more specialist agarose, NuSieve and Metaphor should
both seperate out bands 27bp different. I think FMC produce them (no
affiliation). Used both in the past, nusieve is easier than Metaphor, but
Metaphor gives better separation. Hope this helps. :o)

Jon

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
> 
> 
>