Primer Design for PCR

Ian A. York iayork at
Fri Dec 11 10:13:53 EST 1998

In article <36711D83.38A6A334 at>,
Leihkauf  <leihkauf at> wrote:
>Hello everyone,
>we just started to design primers for PCR but we don't have any
>experience with it. We used a primer design program called MacVector but

This is very definitely my opinion only:  Primers are cheap enough now
that the best way to find a good primer pair to to order a few and try

Running your eye across primers should be enough to catch obvious problems
(inverted repeats, obvious primer pairing).  Beyond that, programs will
increase your odds of finding a good pair somewhat, but I suspect the
improvement is small; and programs will also toss out primers that aren't
perfect on paper (I guess I should say, aren't perfect in RAM), but that
work fine in practice.

I think that ordering by eye--pulling out a handful of plausible
sequences and trying all possible pairs--has an excellent chance of
getting good PCR over the region you need.  Primers cost less than $25 a
pop, so you expand your options over programs and don't lose a lot of

As I say, that's mere opinion.
    Ian York   (iayork at  <>
    "-but as he was a York, I am rather inclined to suppose him a
     very respectable Man." -Jane Austen, The History of England

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