primer design,specificity
Simone Marker
via methods%40net.bio.net
(by marker from rhrk.uni-kl.de)
Tue Apr 10 02:07:46 EST 2007
Hi,
does anyone have experience with primer design for specific PCR
amplification of one member of a multigene familiy?
I want to find primers for one gene of a multigene family, in which the
family members are highly similar. I'm not sure about the
creteria for specificity: how many mismatches for the genes that I don´t
want to amplify are necessary?
I normally avoid primers that have only mismatches in the 5' moiety. But how
many mismatches are necessay at the 3' moiety of the primer to guarantee
specificity for my gene of interest? I tried to chose at least 3 mismatches.
Does a primer that has
only one or two mismatches at the last 3'base(s) and no mismatch at the
residual bases produce a PCR product?
My problem is, that I use the primers also for specific RT reactions, so I
have to consider also that only one primer (and not a pair) must to be
specific.
(Do I have to consider any differences between RT and PCR in general or do I
have to apply the same criteria for primer specificity? I use an RT enzyme
that is able to reverse transcribe at 50-60°C, so that I can adapt my
primers very flexible (normally I use primers with a melting temperature of
55°C and do the RT at 57°C, works well)).
Thank you very much in advance,
Simone
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