Yet more PCR problems

Jason Lei leij at
Tue Feb 7 22:12:37 EST 1995

smori at (Shahram Mori) wrote:
> LMS  (Tel 0635 578411 X2598) (lee.smith at wrote:

> : UNTIL: just before christmas, I ran a titration of target,
> : and all I got were smears. I repeated it (twice), I got smears.
> : I changed all my reagents, smears. I changed my PCR machine, smears.
> : I went back to the beginning, and used my upstream primer with the 
> : other two downstream primers- worked perfectly. A Ha I cried, my
> : primer has gone funny. I ordered more primers. They arrived.
> : I used them. Smears again (and sometimes, absolutely nothing).
> Could it be that your DNA has fragmented? It might be that there is a
> contaminating piece of DNA [ a fragment of the original] where the primer
> binds to and that gives you smear. I would recommend running your DNA on
> agarose to see if there are any other contaminating DNA's there. This is just
> an idea, probably a long shot.

I had a similar situation as encountered by Lee before.  It turned out that the
problem was the change of Taq from company A to company B.  Since I decided not
to reoptimize the PCR condition just for the new Taq, I went back to the 
orginal Taq and my day was back to normal.  I am not sure if this is Lee's
problem, though.

Jason Lei


Postdoc, Horticulture Dept.
Purdue University

Speaking for myself..........

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