[meltsim] [Fwd: methylation?]

Richard.Blake rdblake at ibm.net
Fri Dec 1 11:43:18 EST 2000

We do not have the thermodynamic parameters for
methylated CG nearest neighbors. I suppose they
could be determined from delta Tm, but we would,
of course have to assume that the cytosine
residues of all CG neighbors were methylated.
No. That is incorrect. They would be specified
when the sequence is read in. Actually this question
is almost trivial, but we would need the enthalpy
and entropy values as a function of ionic strength.
I am very much in the middle of something, so
if you have the time could you look through the
literature. No way am I going to measure them.
I think my apparatus is kaput now anyway. 
were meth 
At 10:33 PM 11/30/00 +0000, you wrote:
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>Date: Thu, 30 Nov 2000 12:28:58 -0500
>From: "Dr. Christopher Pearson" <cepearson at genet.sickkids.on.ca>
>Subject: methylation?
>To: jeff at bioinformatics.org
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>To: Jeff
>From:  Christopher E. Pearson, Ph.D. (cepearson at genet.sickkids.on.ca)
>Date:  November 30, 2000
>I was wondering if the Meltism program can account for melting
>differences due to meCpG status.  Methylation of C residues greatly
>increases the melting temperature of DNAs (Ehrlich,M et al., 1975,
>Biochim. biophys. Acta, 395:109-119; Collins,M. & Myers,RM 1987, J. Mol.
>Biol. 198:737-44).  If Meltism does not permit for this variation can it
>be modified?  Are there other programs that may be able to perform such
>an analyses?  Thank you in advance for your assistance on this.
>Christopher E. Pearson, Ph.D.
>Hospital for Sick Children       tel:  (416) 813-8256 (office)
>Department of Genetics         tel:  (416) 813-8170 (lab)
>555 University Avenue          tel:  (416) 813-6384 (secretary)
>Elm Wing, Rm. 11-135          fax:  (416) 813-4931
>Toronto, Ontario               email:  cepearson at genet.sickkids.on.ca
>Canada  M5G 1X8

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