hairpins in PCR primers

Michael N. Nitabach mnitabachnospam at yahoo.cominvalid
Mon Feb 7 23:17:48 EST 2000


Hairpins definitely can affect PCR amplifications and other primer extension
reactions.  When I use primers with significant predicted secondary
structure, I always perform my reactions in triplicate, with  0%, 5%, or 10%
DMSO in each reaction.  In many cases, reactions that give no detectable
product without DMSO work beautifully with DMSO.  My understanding of the
mechanism of the DMSO effect is pretty vague, but I believe it must be due
to a differential effect of the DMSO on intramolecular and intermolecular
base-pairing.
--Mike Nitabach


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.
>
> Regards
>
> Alex
>
> adobrovic at medicine.adelaide.edu.au
>
> ---





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