Inosine in degenerate PCR primers?
rewhlab at cbdn.ca
Fri Mar 3 01:26:11 EST 1995
I have a couple of questions about degenerate PCR. I hope someone
experienced with degenerate PCR can lend me some advice.
I am designing degenerate PCR primers based on aligned protein
sequences (bacterial). I am tring to keep
the degeneracies to around 1000X, however, I end up with short primers
(11-12 mers). Is it ok to use inosine at places of 4-fold degeneracies
to reduce the overall degeneracy of longer primers? If yes, then how will
the incorporation of inosine into primers affect their annealing
temperature? Will it affect any other parameters that I should be aware
of? Any advice on the use and design of degenerate primers would be
bina at unixg.ubc.ca
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