PCR stutters through oligo-A regions

Pamela Norton pnorton at lac.jci.tju.edu
Wed Mar 20 17:32:59 EST 1996


In article <4in1cj$nu6 at majestix.uni-muenster.de>, Juergen Brosius
<RNA.world at uni-muenster.de> wrote:

> Thanks for the idea.  However, we had a similar problem in cDNA clones 
> containing a stretch of 12 C-residues.  In this case we do not know 
> whether the stuttering or slippage was due to reverse transcriptase 
> (first strand) or DNA polymerase (second strand cDNA synthesis) or both.
> Juergen

   Reverse transcriptase is a likely culprit, it has been reported to
stutter at A tracts (U tracts on template RNA), and I have seen this
myself in primer extension reactions. 

   Juergen, it wasn't clear in your original post if you were performing
an RT step prior to the PCR reactions that are giving you trouble, or
whether the starting template is DNA. Which is it?

      Pam Norton

-- 
Pamela A. Norton, Ph.D.          Assistant Professor of Medicine
Thomas Jefferson University
Philadelphia, PA 19107           p_norton at lac.jci.tju.edu



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