module Qu
Thermodynamics Parameters for calculating Tm and Gibbs free energy
References
Matched base-pair => [1] SantaLucia JR (1998) "A unified view of polymer, dumbbell and oligonucleotide DNA nearest-neighbor thermodynamics", Proc Natl Acad Sci 95=>1460-65 http=>//dx.doi.org/10.1073/pnas.95.4.1460. Mismatched base-pair => [1]. Allawi, H.T. and SantaLucia, J. (1997) Thermodynamics and NMR of internal GT mismatches in DNA, Biochemistry, 36, 10581-10594. [2]. Allawi, H.T. and SantaLucia, J. (1998) Nearest-neighbor thermodynamics of internal A center dot C mismatches in DNA=> Sequence dependence and pH effects, Biochemistry, 37, 9435-9444. [3]. Allawi, H.T. and SantaLucia, J. (1998) Nearest neighbor thermodynamic parameters for internal G center dot A mismatches in DNA, Biochemistry, 37, 2170-2179. [4]. Allawi, H.T. and Santalucia, J. (1998) Thermodynamics of internal C center dot T mismatches in DNA, Nucleic Acids Research, 26, 2694-2701. NN model => [1] SantaLucia, J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proceedings of the National Academy of Sci-ences of the United States of America, 95, 1460-1465. [2] von Ahsen, N., Wittwer, C.T. and Schutz, E. (2001) Oligonucleotide melting tempera-tures under PCR conditions=> Nearest-neighbor corrections for Mg2+, deoxynu-cleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas, Clinical Chemistry, 47, 1956-1961.
by Wubin Qu
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