Hints for PCR of A/T-rich sequences?

Manuel Simon ma at ABC.univie.ac.at
Wed Jun 1 11:24:15 EST 1994


In article <199405181215.FAA15227 at net.bio.net> RCARPER%JHUHYG.BITNET at JHUVM.HCF.JHU.EDU (robin carper) writes:
>From: RCARPER%JHUHYG.BITNET at JHUVM.HCF.JHU.EDU (robin carper)
>Subject: Hints for PCR of A/T-rich sequences?
>Date: 18 May 1994 05:15:48 -0700

>I have to do a bunch of PCR on highly A/T rich sequences and was wondering
>if anyone has done any optimization experiments for any of the zillion PCR
>variables, as they relate to A/T sequences.  Lower extension temp? Higher salt?
>Increase gelatin?  Any thoughts on this would be appreciated.


Hi robin,

since AT rich stretches resemble ubiquitous sequences (e.g.TATA box 
like things or 5´untranslated regions in general) and therefore possibly give 
rise to unspec. bands I think the only thing you can really do to increase 
your specificity is to make your primer longer, to be able to anneal at higher 
temperatures.

MA





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