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PCR primer design criteria

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


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.



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