Effect of mismatches on Breslauer Thermodynamics

Dorothy Lowry dlowry at cmu.unige.ch
Fri Jan 15 12:38:20 EST 1993

I would like to open a discussion on DNA melting temperature - in particular
with regard to oligonucleotides.  I would like to design primers for PCR, and
I am currently using the Breslauer nearest neighbour values of entropy and
enthalpy to calculate the Tm based on the nucleotide sequence.

HOWEVER, what if there is a mismatch?  (obviously this is not desirable for
designing primers but it is useful to know if it binds anywhere else...) In
this case, how is the Tm calculated?  I have seen, in Manatius, the suggestion
that 1 degree C should be subtracted for each mismatch (?) but this is based
on the Suggs equation ( Tm = 4 * (GC) + 2 * (AT) etc.) !

I have also recently read a paper that calculated delta G for a sequence that
DID have a mismatch in it and there is NO WAY I can duplicate the math (in 
fact, if I ignore the mismatch completely, I still am off by a factor of 2).
The paper is:

"Use of an RNA Folding Algorithm to Choose Regions for Amplification by the
 Polymerase Chain Reaction". Analytical Biochemistry 185: 57 - 62 (1990).
 Luke Pallansch, Howard Beswick, John Talian, and Peggy Zelenka.

Does anyone have any thoughts on this subject and/or e-mail addresses of any
of the authors?  Any help would be appreciated!


Dorothy Lowry
Dept. Medical Biochemistry
University of Geneva, Switzerland	dlowry at cmu.unige.ch
Graduate student and PC/GENE programmer	phone:  +41 22 70.25.490

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