oligo melting temperatures

Joseph A White whitejo at PILOT.MSU.EDU
Thu May 16 09:47:06 EST 1996


Brian Osborne's response to Bernd Weisshaar's message refers to "nearest
neighbor thermodynamic values" which are included in a program called
PRIMER available from the Whitehead Institute by ftp (ftp.genome.wi.edu).
This program is useful for finding optimal primer locations in a known
sequence, but also can be used to determine oligonucleotide melting temps
using the nearest neighbor method.  I have used the program to do this and
found the Tm data to be reasonably accurate.

Another program, OLIGO, in its latest version may also include the nearest
neighbor values, although older versions do not.  These older version give
rather inaccurate Tm values for oligonucleotides.

Primer version 0.5 runs on PC compatible computers.  I am not sure if there
is a Mac compatible version, but I would guess there is.  Log on and check.
Be aware that the program is copyrighted and free for use by academic
institutions, but not free to commercial organizations.

Joe White

Joe White       (whitejo at pilot.msu.edu)
301 Biochemistry
Michigan State University
East Lansing, MI  48824

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