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PCR primer design criteria

Jfloring at aol.com Jfloring at aol.com
Fri Dec 8 04:22:23 EST 1995

Sarven Sabunciyan <sarven at org.ecc.ubc.ca> wrote:


>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.


I've just begun to use MacVector.  You can easily specify a GC 3' end, or
choose not to, if you wish.  It has a pretty good interface which helps avoid
primer overlap, hairpins, etc.  I like it, so far.

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