PCR primer design software

LEARN at UCRVMS.BITNET LEARN at UCRVMS.BITNET
Tue Sep 1 14:19:00 EST 1992


I apologize to the network for asking a question that is almost an FAQ:

What methods do you all use to design primers for PCR (primarily) and
sequencing?  We have OLIGO v3.4 in our lab and many of us have tried to use it
with mixed results.  My perception of primer design is that it is a "black box."

1) Has anyone done the experiment comparing the use of OLIGO to a seat-of-the-
   pants, intuitive "method?"

2) Our impression with the results of OLIGO is that it may be too finicky.  We
   use primer-pairs that were designed before we bought software.  We have
   tried to use OLIGO to analyze the primers (which work in at least 75% of a
   broad sample of different angiosperm species) and it predicts that they
   might have problems.  Does anyone have the same experience?

3) Are there reviews in the literature that specifically address the issue of
   designing primers for PCR?  We are familiar with "The Simple Fool's Guide to
   PCR" v2.0 by Steve Palumbi and coworkers.  Is there anything that goes
   beyond this to explain theory of primer design?


Any help that you can provide will be greatly appreciated.  I will summarize
responses.

Thanks,

Jerry Learn
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