Inosine in degenerate PCR primers?

Hancock Lab rewhlab at
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
greatly appreciated.

Jim Bina
bina at  

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