Taq DNA Pol and frameshifts

[Hanson Lab]

In article <3439c4$hn1 at usenet.srv.cis.pitt.edu>, mjmst33+ at pitt.edu (Michael
J Marino) wrote:

> Hello all,
> 
> I am currently sequencing some cloned  rt-pcr products and am finding 
> frequent frameshifts.
[large snip]

Michael, are you sure it is the Taq that is doing the frameshift?  I have
seen (and also heard reported at a meeting) that reverse transcriptase can
do some interesting frameshifts-- mostly one or more nt deletions.  In the
cases I have seen these tend to be at certain sequences, often it occurs in
T stretches (coding strand).  I have also seen deletions in PCR (no RT
step) that have been real clean deletions of a repeated sequence.  I
ascribed those to mispriming, but never really tracked it down.  So I guess
I'm not being too helpful, but yes I've seen this, too.
Claudia Sutton  aka cas9 at cornell.edu