hairpins in PCR primers

Csaba Kiss csakis at
Wed Feb 2 04:46:53 EST 2000

I think it is very much dependent on the length of the hairpin and the
sequence of it. When you talk about melting temperature, keep in mind that
it only tells you that half of your DNA is in ss form. Forming a hairpin is
much easier than reassociating two separate DNA strands. So be careful with
the melting temperature, it is only a rule of thumb, not a very accurate

"alex dobrovic" <adobrovic at> wrote in message
> Does anyone know if hairpins in PCR primers really affect PCR
> amplifications? Most PCR reactions would be carried out at a temperature
> far in excess of the melting temperature of the hairpin.
> Regards
> Alex
> adobrovic at
> ---

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