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mean stacking temp. algorithm

Michael Finney mikef at a.crl.com
Fri Feb 14 20:16:37 EST 1997

In article <32FF6942.4377 at midplains.net>, Les Hoffman
<lhoffman at midplains.net> wrote:

>In 1990 Biotechniques vol.8 (6), pp. 674-678, R.A. McGraw et al. 
>presented a method for calculating the melting point of oligos based on 
>nearest-neighbor interactions of the bases.  We have found the 
>hybridization temperatures calculated manually with their methods give 
>very accurate estimates of the Tm of oligos around 20 bases long. We 
>cannot, however, find a source for the software for the algorithms for 
>mean stacking temperature and "T50-hyb", the Tm.  Doing these 
>calculations by hand seems a little ridiculous.  Does anyone out there 
>know where we can download or obtain the software?

There are commercial packages that do it, as well as the free Whitehead
Primer program, but I find all these to be cumbersome. I prefer the
Minnesota web site that performs the calculation:


By the way, the original reference for the method is: Breslauer et al.,
Proc. Nat. Acad. Sci. 83, 3746-50, 1986.

Good luck with your new products, and say Hi to Gary Dahl for me.

Michael Finney, PhD |                     | mikef at mjr.com
MJ Research, Inc.   |     /\/\\_\ /\_\    | 617 370 8112
149 Grove Street    |    /\_\_\\ \\_\     | 617 924 2148 fax
Watertown MA 02172  |          /_/        | www.mjr.com

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