PCR primer instability

[Mark Naylor]

I have been having problems with PCR primer instability lately. I am 
using 21-24 bp single stranded DNA oligo directed against kinase 
inhibitor gene exons (e.g. genomic DNA target) that are inherently 
GC-rich the primers themselves tend to have unusually high GC contents 
(60-70% some of them). These primers are all selected using computer 
software (Oligo, MacVector and Amplify) When we first get the 
primers and put them in solution they work fine, but after a few days, 
the amplification signal drops noticably and shortly thereafter, they 
stop giving signal. We have noticed this on all of our kinase inhibitor 
primers but not on other primers we are using that are made by the same 
synthesis lab. I suspect that intraprimer interactions are responsible 
for this phenomenon. Has anyone else seen anything like this?

Mark Naylor
mnaylor at cclink.net.uokhsc.edu