PCR ghost bands

[HARDIES at THORIN.UTHSCSA.EDU]

X-News: thorin.uthscsa.edu bionet.molbio.methds-reagnts:1383
From: oliver at molgen.biologie.uni-marburg.de (Oliver Sorgenfrei)
Subject:Re: PCR ghost bands
Date: Fri, 24 Jun 1994 13:46:50 GMT
Message-ID:<oliver.18.2E0AE3CA at molgen.biologie.uni-marburg.de>

In article <2uca3i$lp9 at apakabar.cc.columbia.edu> pcj1 at konichiwa.cc.columbia.edu (Pierre Jelenc) writes:
>From: pcj1 at konichiwa.cc.columbia.edu (Pierre Jelenc)
>Subject: PCR ghost bands
>Date: 23 Jun 1994 15:35:14 GMT


>Very often (3/4 of the time), I see a PCR product shorter than the correct
>one.   [stuff deleted]

:Dear Pierre,
:you might have secondary structure in your template, which could lead to 
:deletions upon PCRing. If that is the reason you could prevent that by 
:adding ssb to the reactions.
:For further information see: Q. Chou (1992), NAR, 20: 4371
:Hope this helps.

:Oliver

:==========================================================================
:     Novell-Server Molekulargenetik Biologie Uni-Marburg Deutschland
:==========================================================================

I was under the impression that ssb denatured at PCR temperatures, and that
its beneficial effect was in binding the primers until high temp. was reached
thus effecting a "hot start".  The info came from Cetus, which was pushing
hot-start and discouraging buying (someone else's) ssb at the time, so I 
suppose it is suspect.  Does anyone know?

Steve Hardies      Hardies at thorin.uthscsa.edu