How does oligoprop calculate melting temperature? I can't get it to match.

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Ramsey 2013-7-12

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Hi, I am using the oligoprop function of the bioinformatics toolbox. When I calculate the melting temperature of a random sequence, it gives thermodynamic properties (dH, dS) as well as a melt temperature (Tm). I am trying to get the Tm directly from my thermodynamics properties, based on the SantaLucia Biochemistry (1996) paper. However I am off by about 7C.

Basically, I am calculating the Tm by:

Tm = dH/(R*ln([P])+dS)+12.5*ln([Na+])

with R = 1.98e-3 kcal/mol/K, [Na+,P] as defaults .05, 5e-5 M. Any insight on the difference between the program and the paper (or my method) would be appreciated.

Thanks.

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Answer 1

Ingrid Tigges 2013-7-22

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The oligoprop function uses the calculation from this site: href = ""<http://www.basic.northwestern.edu/biotools/oligocalc.html</a>> (scroll down for formulas) which differs from your calculation calculation. According to my knowledge, it does not calculate Tm based on the paper you mentioned. If you want to have futher information regarding this topic you might want to consider technical support.