Who is wrong with primer design? [long]

Oswaldo oswaldo at iats.csic.es
Wed Aug 2 02:45:53 EST 2000

John Dixon wrote:
> A while back Oswaldo (oswaldo at iats.csic.es) asked about the confusion
> over whether primers for PCR should be made with a 3' GC clamp.

[snipped a great review of what we can call "in primer design, do it as
you wish"]

> Well, thanks. That's really cleared it up then.
> Good luck, Oswaldo.

Hey, thanks for the support!... It is much clearer now. I'll just
continue doing as till now. It works most of the times, anyway. The
problem is that some of the software for primer design scores primers
based on criteria that, like the terminal clamp(s), can be rather
irrelevant. People who uses only those resources and who plays to get
primers with the highest scores should be aware of that.

In my opinion, it is better to focus on the 2ndary structure. Thanks for
the mini review


> JD (no affils to any of above, obviously. all errors my own etc. etc.)
> P.S. FWIW, my preferred offerings to the PCR gods are primers with a
> single G or C 3', FWIW. Seems to keep'em happy most phases of the moon.
> --
> John Dixon                    Lab 44 (1223) 334131
> Wellcome/CRC Institute        Fax 44 (1223) 334089
> Cambridge University
> United Kingdom CB2 1QR       e-m: jpcd100 at mole.bio.cam.ac.uk

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