Who is wrong with primer design?

alex dobrovic adobrovic at medicine.adelaide.edu.au
Tue Aug 1 19:30:58 EST 2000


The summary from John Dixon  is invaluable.

In our lab, we design primers to be used at high annealing temperatures. In
this case GC clamping at the 5' end is useless because if there is not a
high equilibrium favouring pairing at the 3'end, extension will be
compromised.

In addition to overall Tm, I try to have 3 G or Cs in the last 5 3' bases
with at least one of these being iin the last 2 bases.

Finally, this theory needs practical testing by people making all possible
combinations. Any volunteers?

Alexander Dobrovic, Ph.D.
Chief Medical Scientist/Dept of Haematology-Oncology
Affiliate Senior Lecturer/University of Adelaide Dept of Medicine
The Queen Elizabeth Hospital
Woodville, SA 5011, Australia

Tel  61-8-8222 7676
Fax  61-8-8222 6046
alexander.dobrovic at adelaide.edu.au



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