PCR primer design criteria

Sarven Sabunciyan sarven at org.ecc.ubc.ca
Wed Dec 6 21:19:42 EST 1995


Hi!

I have a question about the criteria used to design PCR primers.  I know
you should avoid hairpin loops, primer dimerization and avoid primers
which will anneal to other transcripts.  I've also read (and been told)
that a primer should not have a T at the 3 prime end since this will
result in non-specific annealing.  I've been asking for demo versions of
commercially available primer design packages as well as using shareware
programs (by the way, I am working on a Mac).  Several of these programs
have given me primers with T's at the 3 prime end.  In fact when I asked
a friend who uses Oligo to come up with primers, Oligo gave a primer with
a T at the end (granted it was an older version of the program). Is a T 
at the 3 prime end of a primer not all that crutial for specific PCR or
are these programs not all that reliable?  Can somebody give me
references about designing primers?  Any help is much appreciated.

Thanks

Sarven



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