Tm and PCR optimization

Bill Engels wrengels at facstaff.wisc.edu
Sat Feb 26 17:37:30 EST 1994


In article <1994Feb14.142130.1 at molbiol.ox.ac.uk>, rhubner at molbiol.ox.ac.uk
wrote:

>  I used the 2+4 rule to calculate an approximative Tm and checked this one
> with the program PRIMER 0.5 (I suppose - probably wrong- that this program
> uses the (long) DNA formula with + 16.6 [Na+] etc...

26 February 1994

I looked at the source code of PRIMER 0.5 which LanderÕs lab has posted at
genome.wi.edu. They estimate Tm by a method that sums values of nucleotide
neighbors to compute entropy and enthalpy. I don't know where these values
come from, but here they are. (Version 2.0 of Amplify will use this same
approach for Tm if it seems to work better empirically.)

Entropy values
          N         A         C         G         T
N         215       239       208       173       169
A         168       240       129       135       169
C         210       173       266       267       135
G         220       208       278       266       129
T         215       239       208       173       240

Enthalpy values
          N         A         C         G         T
N         78        86        78        65        60
A         81        91        58        56        60
C         105       65        110       111       56
G         94        78        119       110       58
T         78        86        78        65        91

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William R. Engels                     :     WREngels at facstaff.wisc.edu
Genetics Department, 445 Henry Mall   :         office: (608) 263-2213
University of Wisconsin               :            lab: (608) 262-5578
Madison, WI  53706                    :            FAX: (608) 262-2976
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