reducing secondary structures in long PCR primers

Dr. Duncan Clark Duncan at
Fri Jun 16 04:11:27 EST 2000

In article <8ibk48$n2l$1 at>, Benny Lo
<benny at> writes
>What I suspect here is that the restriction sequence was "looping out" in
>the primer during the PCR process so the Taq enzyme could not extend
>properly at that position.

What happens when you put your primer sequence against say Mfold. Do you
have such loops?

Alternatives are that you received  poorly synthesised primer with no
Hind III site in or that you have a nuclease in your ligation that is
chewing up the ends of the insert.

The problem with being on the cutting edge is that you occasionally get 
sliced from time to time....

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

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