PCR Puzzler

Ross Feldberg rfeldber at Tufts.edu
Wed Nov 15 11:23:36 EST 2000

Hi all,

Here is a little PCR Puzzler (with apologies to Tom and Ray) that  my
local PCR mechanics have not been able to solve.

I am amplifying a peptide receptor in rat prostate and typically get the
predicted product of 500 bp. However, there is usually a minor band at
600 bp. I never gave this much thought since there is a possible false
priming site, which would give a minor product at that size. However,
the other week I surveyed several tissues and discovered that in some
tissues this minor product was absent or greatly reduced while in one
tissue (spleen)  the minor product was much more prevalent than the 500
bp product.

Great, I thought ? alternate splicing or some related but new receptor.
However, when I gel purified the 600 bp band from spleen and then
reamplified it, what I got was a major product at 500 bp and a minor
product at 600 bp. So it looks like false priming again. But why would I
see tissue specificity for false priming and the minor product?

Any ideas from you PCR aficionados out there?

Ross Feldberg
Dept of Biology
Tufts University

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