Ming-Piao Kao wrote:
> Does anyone know how one can determine the melting-temperature
> of 2 DNA-strands which have several mismatches between them ??
> And is this possible using GCG software(to which I have access) ?
> Thank you very much for any help,
> De'de' Kao
>mingpiao at sci.kun.nl
When I did my dissertation (in computer science in 1992-1994),
I was assisting biologists who were using this equation:
Given:
[Na+] the sodium ion concentration
percent G+C the percent G and C in the sequence
size the length of the sequence
Compute Tm in degrees centigrade as:
Tm = 79.8 + 18.5*Log[Na+] + 58.4*(percent G+C) - 820/size
Which was given in:
Schleicher and Schuell,
"Transfer and Immobilization of Nucleic Acids
to S&S Solid Supports"
Schleicher and Schuell, Keene, NH, 1987
This source referenced:
Birnstiel M.L., Sells, B.H., and Purdom, I.F
"Kinetic Complexity of RNA molecules"
J. Mol. Biol. 63 (1972) 21-39
and
Casey J., and Davidson, N.
"Rates of formation and thermal stabilities of RNA:DNA
and DNA:DNA duplexes at high concentrations of formamide"
Nucleic Acids Research, 4 (1977) 1539-1552.
However, in my dissertation, a "personal communication" (from one
of the biologists I was assisting) informed me that Tm computed
with this equation was found to be "insufficient" for predicting
actual behaviors; in this case, these were probes for in-situ
hybridization of rRNA.
Without local access to journals, I feel as if I am
giving the melting point of phlogiston rather than DNA and
I expect that this problem has been investigated since then.
So, I would be very interested in hearing from others on
the computation of Tm.
On the other part of the question: I do not have or use GCG
and cannot comment on how Tm might be obtained with it.
Peter J. Floriani, Ph.D.
floriani at epix.net
----------------------------------------------------
I deny that biology can destroy the sense of truth,
which alone can even desire biology. No truth which
I can find can deny that I am seeking the truth.
My mind cannot find anything which denies my mind.
G. K. Chesterton, "The Long Bow" in Collected Works 14:96
