Unknown Primer

Dr. Duncan Clark news at hgmp.mrc.ac.uk
Tue Jun 26 06:59:04 EST 2001

In article <3B3858E5.AD554BC3 at utanet.at>, the eminent Thomas Mohr at
Vienna University, Austria wrote
>We did RT-PCR for TGF-beta1 to test whether TGF-beta1 expression was
>downregulated on mRNA level by a certain drug.
>Due to a mistake, one primer contained a mmismatch at the 3' end. The
>mRNA we found was of different length than it should be (approx. 200Bp
>instead of 125) and could be downregulated by our drug (contrary to
>TGF-beta). We would be interested in finding out which protein does
>belong to this mRNA. Since we're not very well accoustomed with
>available databases, we would be very grateful for any hints how to do

You need sequence data for the RT-PCR product you now have. I would
suggest TA cloning it and having it sequenced. I would then blast the
sequence against a database.

You can always try blasting your incorrect primer pair and seeing
whether they show up a 200bp mRNA. 

Sequencing is the real foolproof way of finding what you have.


The problem with the gene pool is that there is no lifeguard.

Duncan Clark
GeneSys Ltd.
Tel: +44(0)1252376288
FAX: +44(0)8701640382

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