Primer-dimer problems

Chris Zarow zarow at molbio.usc.edu
Wed Aug 23 16:25:20 EST 1995


Greetings, All.

     I am getting inconsistent results with a primer set which
should give me a single band of about 550 bp.  One thing I have
noticed is the existence of primer-dimers and and primer ladders
(up to 3 bands) in the lanes where I get little or no specific
product.  
     I know that primer-dimers can be favored when the
annealing temperature is too low or the Taq or primer
concentrations are too high.  Primer Tms are both 53.7	; product
Tm (calculated) is 77.9	.  I saw no product with an annealing
temp of 65	 but a nice band at 60	.  I routinely use 0.4 units of
Taq polymerase (in the form of TaqStart) and 25 pmol of each
primer per 50 æl reaction.  
     What else can favor primer-dimer formation?  I'm thinking
that if I can push the conditions away from primer-dimers I might
get more product.
-- 
Chris Zarow, Ph.D
University of Southern California
Rancho Los Amigos Medical Center
zarow at molbio.usc.edu



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