PCR artifact?

Klaus Salger salger at zi.biologie.uni-muenchen.de
Fri Jun 21 14:11:20 EST 1996

Dear netters,

a colleague down the hall has the following problem.

She wants to amplify a neuropeptide precursor which contains short
repeats of 5 amino acids. She used degenerate primers and got a product
which contains 9 repeats that would fit her primer sequences seperated
by 4 nucleotides that are not in the primer.
So it looks like this:
<degenerate primer sequence> GATC <degenerate primer sequence> GATC ...

The primer sequences are different in the repeats (degenerate), the
extra 4 bases are always the same.
There is also an open reading frame which looks more or less like what
she was looking for.

Now the question is if this is likely to be a PCR artifact.
Can anybody explain where the extra 4 bases might have come from? Did
anybody get something like this?

Thanks in advance

Klaus Salger                phone : +49 (0)89 5902 -502
Zoologisches Institut       FAX   :                -450
AG MacWilliams              e-mail: salger at zi.biologie.uni-muenchen.de
Luisenstr. 14               
80333 Muenchen

BioLinks: http://www.zi.biologie.uni-muenchen.de/~salger/salger.html

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