PRIMER: melting points

micha at myhost.subdomain.domain micha at myhost.subdomain.domain
Wed Aug 10 16:10:37 EST 1994

ajb at seqnet.dl.ac.uk wrote:
: Does anyone have a citation for the basis of the melting point calculation
: used in the PRIMER program?

- supposed you are talking about the Whitehead Institute Primer program ... -
A guy in our lab (working often with PCR and using Primer, even having
ported it to the PC) says it is using the same formula as appears in 
Maniatis' Molecular Cloning - including corrections for oligonucleotides.

The Q&A document, however, says it is _not_ using GC/AT ratios but thermo-
dynamic data ...

We will check this out, but we are running PRIMER 0.5, so YMMV :-)

: Thanks in Advance

: Alan Bleasby
: daresbury

By the way:
A recent description of good combinations of thermodynamic parameters
was recently published in

Nucleic Acids Research, 1994, Vol. 22 No. 14 pp 2760-2768
G. Steger :
Thermal denaturation of double-stranded nucleic acids:
prediction of temperatures critical for gradiemt gel electrophoresis
and polymerase chain reaction

together with description of a program based on D. Poland's algorithm
calculating thermal stability and denaturation behaviour.

There is also a GCG version of the program, more info on request!

Hope this helps,

	Michael Schmitz
	Biophysics, U. Duesseldorf

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