problems with PCR

[stephen nurrish]

In article <2u4ed7$lr2 at mserv1.dl.ac.uk>, WMGDDM <WMGDDM at CARDIFF.AC.UK>
wrote:

> I've got a problem with a PCR that I'm attempting...
> 
>     I'm trying to use a pair of primers to follow a series 
> of deletions that I'm making in a plasmid.
>     
>     Under 'standard' conditions I can amplify the deleted 
> version of the plasmid but not the original undeleted 
> version.
> 
>     Can anyone explain this, I've tried all the usual 
> variations in the reaction conditions, etc. with no luck!
> 
 Is the deleted bit very GC rich, if so this can screw up even Taq.
We've had a lot of problems with particularly GC regions in the 5' end of
the SRF gene. Making the reaction 2.5% formamide got over our problem.

Steve Nurrish