Dr. Hiranya S. Roychowdhury hroychow at
Thu Jul 29 10:17:44 EST 2004

Few primers will sho sero dimer or hp loop formation.  The key is to look at 
the delta-G of the pairings and decide from there which ones should have the 
least dimer/loop problems at the annealing temp. you will be using.

And, shorter overlaps are "in general" better, but that tells you little, 

It is better yet that you read up on PCR principles  thoroughly before diving 
into it.

Quoting jmfopouk at

> Hi, am getting confused about avoiding primer-dimer formation during primer
> design. The 
> software (Primer Express) displays primers' secondary structures  and the
> primer-dimer that 
> might be able to form. I wonder wether the best primers combination is the
> one showing short or 
> long overhangs!!!
> Thanks for helping.
> josué

Hiranya S. Roychowdhury, Ph.D.
Coll. Asst. Professor,
Molecular Biology,
Dept. of Chemistry & Biochemistry
Rm# 336, Chemistry Bldg.; MSC 3MLS
New Mexico State University
Las Cruces, NM 88003

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