hairpins in PCR primers

Rafael Maldonado rmaldonado at
Wed Feb 2 09:47:02 EST 2000

alex dobrovic wrote:
> 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.


If the hairpin is small, don't worry, but you have to take in account
that hairpins are made of palindroms, so two primers can anneal each
other, making the melting temperature of that structure higher than
those of a hairpin.


Rafael Maldonado
Divison of Genetics
University of Alicante (Spain)

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