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\newblock Thermodynamics and {NMR} of internal {G-T} mismatches in {DNA}.
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\bibitem{Allawi_37_9435_1998}
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\bibitem{Allawi_37_2170_1998}
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\newblock Nearest neighbor thermodynamics parameters for internal {G.A}
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\bibitem{Allawi_26_2694_1998}
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\newblock Thermodynamics of internal {C.T} mismatches in {DNA}.
\newblock {\em Biochemistry}, 26:2694--2701, 1998.

\bibitem{Asanuma_49_35_2005}
Hiroyuki Asanuma, Daijiro Matsunaga, and Makoto Komiyama.
\newblock Clear-cut photo-regulation of the formation and dissociation of the
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\newblock {\em Nucleic acids Symposium Series}, 49:35--36, 2005.

\bibitem{Badhwar_46_14715_2007}
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\newblock Thermodynamic characterization of {RNA} duplexes containing naturally
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\newblock {\em Biochemistry}, 46:14715--14724, 2007.

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\newblock Thermal stability of {DNA}.
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\newblock Thermodynamic effects of formamide on {DNA} stability.
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\newblock Denaturation of {DNA}.
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\newblock Non-nearest-neighbor dependence of stability for {RNA} bulge loops
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\newblock Thermodynamic parameters for {DNA} sequences with dangling ends.
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\newblock Predicting {DNA} duplex stability from the base sequence.
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\newblock Analysis of repeating {DNA} sequences by reassociation.
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\newblock Rates of formation and thermal stabilities of {RNA:DNA} and {DNA:DNA}
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\newblock Testing the nearest neighbor model for canonical {RNA} base pairs:
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\newblock dimethyl sulfoxide-mediated primer tm reduction : a method for
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\newblock {\em Analytical Biochemistry}, 209:284--290, 1993.

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\newblock Thermal denaturation of {DNA} from bromodeoxyuridine substitued
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\bibitem{Davis_46_13425_2007}
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\newblock Thermodynamic characterization of single mismatches found in
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\newblock {\em Biochemistry}, 46:13425--13436, 2007.

\bibitem{Davis_47_10178_2008}
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\newblock Thermodynamic characterization of naturally occurring {RNA} single
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\newblock {\em Biochemistry}, 47:10178--10187, 2008.

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\newblock Thermal stability and renaturation of {DNA} in dimethyl
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\newblock {\em Biopolymers}, 19:1315--1327, 1980.

\bibitem{Frank_10_2623_1971}
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\newblock Simplification of the empirical relationship between melting
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\newblock {\em Biopolymers}, 10:2623--2624, 1971.

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\newblock {\em Biochemistry}, 83:9373--9377, 1986.

\bibitem{Hall_16_95_1980}
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\newblock Evolution of sea urchin non-repetitive {DNA}.
\newblock {\em J Mol Evol}, 16:95--110, 1980.

\bibitem{Hutton_4_3537_1977}
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\newblock Renaturation kinetics and thermal stability of {DNA} in aqueous
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\bibitem{Junji_29_3289_2001}
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\newblock Thermodynamic stability of base pairs between {2-hydroxyadenine} and
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\newblock {\em Nucleic acids research}, 29:3289--3296, 2001.

\bibitem{Kierzek_34_3609_2006}
Elzbieta Kierzek, David~H. Mathews, Anna Ciesielska, Douglas~H. Turner, and
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\newblock Nearest neighbor parameters for {Watson Crick} complementary
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\newblock {\em Nucleic acids research}, 34:3609--3614, 2006.

\bibitem{Lu_34_4912_2006}
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\newblock A set of nearest neighbor parameters for predicting the enthalpy
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\newblock {\em Nucleic Acids Research}, 34:4912--4924, 2006.

\bibitem{Magdalena_44_10873_2005}
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\newblock Thermodynamic stability of {RNA} structures formed by {CNG}
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\newblock {\em Biochemistry}, 44:10873--10882, 2005.

\bibitem{Marmur_5_109_1962}
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\newblock Determination of the base composition of deoxyribonucleic acid from
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\newblock {\em J. Mol. Biol.}, 5:109--118, 1962.

\bibitem{Mathews_288_911_1999}
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\newblock Expanded sequence dependence of thermodynamic parameters improves
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\newblock {\em J. Mol. Biol}, 288:911--940, 1999.

\bibitem{McConaughy_8_3289_1969}
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\newblock Nucleic acid reassociation in formamide.
\newblock {\em Biochemistry}, 8:3289--3295, 1969.

\bibitem{McTigue_43_5388_2004}
Patricia~M. McTigue, Raymond~J. Peterson, and Jason~D. Kahn.
\newblock Sequence-dependent thermodynamic parameters for locked nucleic acid
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\newblock {\em Biochemistry}, 43:5388--5405, 2004.

\bibitem{Miller_36_5652_2008}
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\newblock Thermodynamic analysis of {5 and 3 single- and 3 double-nucleotide}
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\newblock {\em Nucleic Acids research}, 36:5652--5659, 2008.

\bibitem{Mitsuhashi_10_277_1996}
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\newblock Technical report: Part 1. basic requirements for designing optimal
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\newblock {\em J. Clin. Lab. Anal}, 10:277--284, 1996.

\bibitem{Musielski_21_447_1981}
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\newblock Influence of dimethylsulfoxide on transcription by bacteriophage
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\newblock {\em Z allg Microbiol}, 21:447--456, 1981.

\bibitem{Ohmichi_124_10367_2002}
Tatsuo Ohmichi, Shu-ichi Nakano, Daisuke Miyoshi, and Naoki Sugimoto.
\newblock Long {RNA} danglingend has large energetic contribution to duplex
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\newblock {\em J. Am. Chem. Soc.}, 124:10367--10372, 2002.

\bibitem{O_toole_34_3338_2006}
Amanda~S. O'toole, Stacy Miller, Nathan Haines, M.~Coleen Zink, and Martin~J
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\newblock Comprehensive thermodynamic analysis of {3'} double-nucleotide
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\newblock {\em Nucleic Acids research}, 34:3338--3344, 2006.

\bibitem{O_toole_11_512_2005}
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\newblock Stability of {3'} double nucleotide overhangs that model the {3'}
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\newblock {\em RNA}, 11:512--516, 2005.

\bibitem{Owczarzy_47_5336_2008}
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\newblock Predicting stability of {DNA} duplexes in solutions containing
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\newblock {\em Biochemistry}, 47:5336--5353, 2008.

\bibitem{Owczarzy_50_9352_9367}
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\newblock Stability and mismatch discrimination of locked nucleic acid {DNA}
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\newblock {\em Biochemistry}, 50:9352--9367, 2011.

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\newblock Effects of sodium ions on dna duplex oligomers: Improved predictions
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\newblock {\em Biochemistry}, 43:3537--3554, 2004.

\bibitem{Owen_7_503_1969}
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\newblock Determination of {DNA} base compositions from melting profiles in
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\newblock {\em Biopolymers}, 7:503--516, 1969.

\bibitem{Peyret_5_2000}
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\newblock Prediction of nucleic acid hybridization : parameters and algorithms.
\newblock {\em Ph.D Thesis 4.2, 128, Wayne State University, Detroit, MI.}, 5,
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\newblock Nearest neighbor thermodynamics and {NMR} of {DNA} sequences with
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\newblock {\em Biochemistry}, 38:3468--3477, 1999.

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\newblock Electrostatic effects on polynucleotide {transitions. I. Behavior} at
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\newblock {\em Biopolymers}, 5:975--992, 1967.

\bibitem{SantaLucia_95_1460_1998}
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\newblock A unified view of polymer, dumbbell, and oligonucleotide {DNA}
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\newblock {\em Proc Natl Acad Sci USA}, 95:1460--1465, 1998.

\bibitem{SantaLucia_33_415_2004}
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\newblock The thermodynamics of {DNA} structural motifs.
\newblock {\em Annu. Rev. Biophys. Struct}, 33:415--440, 2004.

\bibitem{SantaLucia_35_3555_1996}
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\newblock Improved nearest-neighbor parameters for predicting {DNA} duplex
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\newblock {\em Biochemistry}, 35:3555--3562, 1996.

\bibitem{Schildkraut_3_195_1965}
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\newblock Dependence of the melting temperature of {DNA} on salt concentration.
\newblock {\em Biopolymers}, 3:195--208, 1965.

\bibitem{Sugimoto_354_74_1994}
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\newblock {RNA/DNA} hybrid duplexes with identical nearest-neighbor base-pairs
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\newblock {\em FEBS Letters}, 354:74--78, 1994.

\bibitem{Sugimoto_34_11211_1995}
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\newblock Thermodynamic parameters to predict stability of {RNA/DNA} hybrid
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\newblock {\em Biochemistry}, 34:11211--11216, 1995.

\bibitem{Sugimoto_24_4501_1996}
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\newblock Improved thermodynamic parameters and helix initiation factor to
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\newblock {\em Nuc Acids Res}, 24:4501--4505, 1996.

\bibitem{Tan_90_1175_2006}
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\newblock Nucleic acid helix stability: effects of salt concentration, cation
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\bibitem{Tan_92_3615_2007}
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\newblock Rna helix stability in mixed {Na+/Mg2+} solutions.
\newblock {\em Biophysical Journal}, 92:3615--3632, 2007.

\bibitem{Tanaka_43_7143_2004}
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\newblock Thermodynamic parameters based on a nearest neighbor model for {DNA}
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\newblock {\em Biochemistry}, 43:7143--7150, 2004.

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\newblock Oligonucleotide melting temperatures under {PCR} conditions :
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\newblock {\em Clinical Chemistry}, 47:1956--1961, 2001.

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\newblock Molecular hybridization of immobilized nucleic acids: theoretical
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\newblock Nearest-neighbor thermodynamics of deoxyinosine pairs in {DNA}
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\newblock {\em Nuc Acids Res}, 33:6258--6267, 2005.

\bibitem{Watkins_39_1894_2011}
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\newblock Thermodynamic contributions of single internal {rA.dA}, {rC.dC},
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\newblock {\em Nucleic Acids Research}, 39:1894--1902, 2011.

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\bibitem{Xia_37_14719_1998}
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\end{thebibliography}
