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}

@article{owen_determination_1969,
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}

@article{wahl_molecular_1987,
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@article{allawi_nearest_1998,
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	month = feb,
	year = {1998},
	pages = {2170--2179},
}

@article{allawi_thermodynamics_1997,
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	number = {34},
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	author = {Allawi, Hatim T. and SantaLucia, John},
	month = aug,
	year = {1997},
	pages = {10581--10594},
}

@article{record_electrostatic_1967,
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	year = {1967},
	pages = {975--992},
}

@article{allawi_nearest-neighbor_1998,
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	volume = {37},
	shorttitle = {Nearest-{Neighbor} {Thermodynamics} of {Internal} {A}\ifelse{html}{\out{&middot;}}{\eqn{\cdot}}{C} {Mismatches} in {DNA}},
	number = {26},
	journal = {Biochemistry},
	author = {Allawi, Hatim T. and SantaLucia, John},
	month = jun,
	year = {1998},
	pages = {9435--9444},
}

@article{freier_improved_1986,
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	volume = {83},
	number = {24},
	journal = {Proceedings of the National Academy of Sciences},
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	pages = {9373},
}

@article{santalucia_unified_1998,
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	number = {4},
	journal = {Proceedings of the National Academy of Sciences},
	author = {SantaLucia, John},
	month = feb,
	year = {1998},
	pages = {1460},
}

@article{breslauer_predicting_1986,
	title = {Predicting {DNA} duplex stability from the base sequence},
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	number = {11},
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	year = {1986},
	pages = {3746},
}

@article{von_ahsen_oligonucleotide_2001,
	title = {Oligonucleotide melting temperatures under {PCR} conditions: {Nearest}-neighbor corrections for {Mg2}+, deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas},
	volume = {47},
	copyright = {(C) 2001 The American Association for Clinical Chemistry},
	shorttitle = {Oligonucleotide {Melting} {Temperatures} under {PCR} {Conditions}},
	language = {en},
	number = {11},
	journal = {Clinical Chemistry},
	author = {von Ahsen, Nicolas and Wittwer, Carl T. and Schutz, Ekkehard},
	month = nov,
	year = {2001},
	pages = {1956--1961},
}

@article{ohmichi_long_2002,
	title = {Long {RNA} dangling end has large energetic contribution to duplex stability},
	volume = {124},
	number = {35},
	journal = {Journal of the American Chemical Society},
	author = {Ohmichi, Tatsuo and Nakano, Shu-ichi and Miyoshi, Daisuke and Sugimoto, Naoki},
	month = sep,
	year = {2002},
	pages = {10367--10372},
}

@article{tanaka_thermodynamic_2004,
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	number = {22},
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	month = jun,
	year = {2004},
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}

@article{owczarzy_predicting_2008,
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	volume = {47},
	number = {19},
	journal = {Biochemistry},
	author = {Owczarzy, Richard and Moreira, Bernardo G. and You, Yong and Behlke, Mark A. and Walder, Joseph A.},
	month = may,
	year = {2008},
	pages = {5336--5353},
}

@article{chen_testing_2012,
	title = {Testing the nearest neighbor model for canonical rna base pairs: {Revision} of {GU} parameters},
	volume = {51},
	shorttitle = {Testing the {Nearest} {Neighbor} {Model} for {Canonical} {RNA} {Base} {Pairs}},
	language = {en},
	number = {16},
	journal = {Biochemistry},
	author = {Chen, Jonathan L. and Dishler, Abigael L. and Kennedy, Scott D. and Yildirim, Ilyas and Liu, Biao and Turner, Douglas H. and Serra, Martin J.},
	month = apr,
	year = {2012},
	pages = {3508--3522},
}

@article{watkins_thermodynamic_2011,
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	volume = {39},
	language = {en},
	number = {5},
	journal = {Nucleic Acids Research},
	author = {Watkins, Norman E. and Kennelly, William J. and Tsay, Mike J. and Tuin, Astrid and Swenson, Lara and Lee, Hyung-Ran and Morosyuk, Svetlana and Hicks, Donald A. and SantaLucia, John},
	month = mar,
	year = {2011},
	pages = {1894--1902},
}

@article{mitsuhashi_technical_1996,
	title = {Technical report: {Part} 1. {Basic} requirements for designing optimal oligonucleotide probe sequences},
	volume = {10},
	number = {5},
	journal = {Journal of Clinical Laboratory Analysis},
	author = {Mitsuhashi, Masato},
	year = {1996},
	pages = {277--284},
}

@article{davis_thermodynamic_2007,
	title = {Thermodynamic characterization of single mismatches found in naturally occurring {RNA}},
	volume = {46},
	number = {46},
	journal = {Biochemistry},
	author = {Davis, Amber R. and Znosko, Brent M.},
	month = nov,
	year = {2007},
	pages = {13425--13436},
}

@article{mcconaughy_nucleic_1969,
	title = {Nucleic acid reassociation in formamide},
	volume = {8},
	number = {8},
	journal = {Biochemistry},
	author = {McConaughy, Betty L and Laird, CDo and McCarthy, Brian J},
	year = {1969},
	pages = {3289--3295},
}

@article{santalucia_improved_1996,
	title = {Improved nearest-neighbor parameters for predicting {DNA} duplex stability},
	volume = {35},
	number = {11},
	journal = {Biochemistry},
	author = {SantaLucia, John,  and Allawi, Hatim T. and Seneviratne, P. Ananda},
	month = jan,
	year = {1996},
	pages = {3555--3562},
}

@article{wright_nearest_2007,
	title = {Nearest neighbor parameters for inosine\ifelse{html}{\out{&middot;}}{\eqn{\cdot}}uridine pairs in {RNA} duplexes},
	volume = {46},
	number = {15},
	journal = {Biochemistry},
	author = {Wright, Daniel J. and Rice, Jamie L. and Yanker, Dawn M. and Znosko, Brent M.},
	month = apr,
	year = {2007},
	pages = {4625--4634},
}

@article{chester_dimethyl_1993,
	title = {Dimethyl sulfoxide-mediated primer {Tm} reduction: {A} method for analyzing the role of renaturation temperature in the polymerase chain reaction},
	volume = {209},
	number = {2},
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	author = {Chester, N. and Marshak, D.R.},
	month = mar,
	year = {1993},
	pages = {284--290},
}

@article{tan_nucleic_2006,
	title = {Nucleic acid helix stability: {Effects} of salt concentration, cation valence and size, and chain length},
	volume = {90},
	number = {4},
	journal = {Biophysical Journal},
	author = {Tan, Zhi-Jie and Chen, Shi-Jie},
	month = feb,
	year = {2006},
	pages = {1175--1190},
}

@article{blose_non-nearest-neighbor_2007,
	title = {Non-nearest-neighbor dependence of stability for {RNA} bulge loops based on the complete set of group i single nucleotide bulge loops},
	volume = {46},
	number = {51},
	journal = {Biochemistry},
	author = {Blose, Joshua M and Manni, Michelle L and Klapec, Kelly A and Stranger-Jones, Yukiko and Zyra, Allison C and Sim, Vasiliy and Griffith, Chad A and Long, Jason D and Serra, Martin J},
	month = dec,
	year = {2007},
	pages = {15123--15135},
}

@article{tan_rna_2007,
	title = {{RNA} helix stability in mixed {Na}(+)/{Mg}(2+) solution},
	volume = {92},
	number = {10},
	journal = {Biophysical Journal},
	author = {Tan, Zhi-Jie and Chen, Shi-Jie},
	month = may,
	year = {2007},
	pages = {3615--3632},
}

@article{mctigue_sequence-dependent_2004,
	title = {Sequence-dependent thermodynamic parameters for locked nucleic acid ({LNA})-{DNA} duplex formation},
	volume = {43},
	number = {18},
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	author = {McTigue, Patricia M. and Peterson, Raymond J. and Kahn, Jason D.},
	month = may,
	year = {2004},
	pages = {5388--5405},
}

@article{xia_thermodynamic_1998,
	title = {Thermodynamic parameters for an expanded nearest-neighbor model for formation of {RNA} duplexes with {Watson}-{Crick} base pairs},
	volume = {37},
	number = {42},
	journal = {Biochemistry},
	author = {Xia, Tianbing and SantaLucia, John and Burkard, Mark E. and Kierzek, Ryszard and Schroeder, Susan J. and Jiao, Xiaoqi and Cox, Christopher and Turner, Douglas H.},
	month = oct,
	year = {1998},
	pages = {14719--14735},
}

@phdthesis{peyret_prediction_2000,
	address = {Detroit, MI},
	type = {Ph.{D}. {Thesis}},
	title = {Prediction of nucleic acid hybridization: {Parameters} and algorithms},
	school = {Wayne State University},
	author = {Peyret, Nicolas},
	year = {2000},
}

@article{schildkraut_dependence_1965,
	title = {Dependence of the melting temperature of {DNA} on salt concentration},
	volume = {3},
	language = {en},
	number = {2},
	journal = {Biopolymers},
	author = {Schildkraut, Carl and Lifson, Shneior},
	month = apr,
	year = {1965},
	pages = {195--208},
}

@article{otoole_comprehensive_2006,
	title = {Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring {Watson}-{Crick} terminal base pairs},
	volume = {34},
	language = {en},
	number = {11},
	journal = {Nucleic Acids Research},
	author = {O'Toole, Amanda S. and Miller, Stacy and Haines, Nathan and Zink, M. Coleen and Serra, Martin J.},
	month = jan,
	year = {2006},
	pages = {3338--3344},
}

@article{miller_thermodynamic_2008,
	title = {Thermodynamic analysis of 5' and 3' single- and 3' double-nucleotide overhangs neighboring wobble terminal base pairs},
	volume = {36},
	language = {en},
	number = {17},
	journal = {Nucleic Acids Research},
	author = {Miller, Stacy and Jones, Laura E. and Giovannitti, Karen and Piper, Dan and Serra, Martin J.},
	month = oct,
	year = {2008},
	pages = {5652--5659},
}

@article{otoole_stability_2005,
	title = {Stability of 3' double nucleotide overhangs that model the 3' ends of {siRNA}},
	volume = {11},
	language = {en},
	number = {4},
	journal = {RNA},
	author = {O'Toole, Amanda S. and Miller, Stacy and Serra, Martin J.},
	month = jan,
	year = {2005},
	pmid = {15769878},
	pages = {512--516},
}

@article{santalucia_thermodynamics_2004,
	title = {The thermodynamics of {DNA} structural motifs},
	volume = {33},
	number = {1},
	journal = {Annual Review of Biophysics and Biomolecular Structure},
	author = {SantaLucia, John and Hicks, Donald},
	month = may,
	year = {2004},
	pages = {415--440},
}

@article{escara_thermal_1980,
	title = {Thermal stability and renaturation of {DNA} in dimethyl sulfoxide solutions: {Acceleration} of the renaturation rate},
	volume = {19},
	shorttitle = {Thermal stability and renaturation of {DNA} in dimethyl sulfoxide solutions},
	language = {en},
	number = {7},
	journal = {Biopolymers},
	author = {Escara, June F. and Hutton, James R.},
	month = jul,
	year = {1980},
	pages = {1315--1327},
}

@article{badhwar_thermodynamic_2007,
	title = {Thermodynamic characterization of {RNA} duplexes containing naturally occurring 1 * 2 nucleotide internal loops},
	volume = {46},
	number = {50},
	journal = {Biochemistry},
	author = {Badhwar, Jaya and Karri, Saradasri and Cass, Cody K. and Wunderlich, Erica L. and Znosko, Brent M.},
	month = dec,
	year = {2007},
	pages = {14715--14724},
}

@article{dumousseau_melting_2012,
	title = {{MELTING}, a flexible platform to predict the melting temperatures of nucleic acids},
	volume = {13},
	journal = {BMC Bioinformatics},
	author = {Dumousseau, Marine and Rodriguez, Nicolas and Juty, Nick and Le Novere, Nicolas},
	month = may,
	year = {2012},
	pages = {101},
}

@article{le_novere_melting_2001,
	title = {{MELTING}, computing the melting temperature of nucleic acid duplex},
	volume = {17},
	abstract = {Summary: MELTING computes the enthalpy and entropy of an
 oligonucleotide duplex helix-coil transition, and then its
 melting temperature. The program uses the method of
 nearest-neighbours. The set of thermodynamic parameters can be easily
 customized. The program provides several correction methods for the
 concentration of salt. MELTING is a free program, available at no
 cost and open-source. Perl scripts are provided to show how MELTING
 can be used to construct more ambitious programs.Availability: MELTING is available for several platforms
  (http://www.pasteur.fr/recherche/unites/neubiomol/meltinghome.html)
  and is accessible via a www server (http://bioweb.pasteur.fr/seqanal/interfaces/melting.html).Contact: nl223@cus.cam.ac.uk},
	language = {en},
	number = {12},
	journal = {Bioinformatics},
	author = {Le Novere, Nicolas},
	month = dec,
	year = {2001},
	pages = {1226--1227},
}

@article{frank-kamenetskii_simplification_1971,
	title = {Simplification of the empirical relationship between melting temperature of {DNA}, its {GC} content and concentration of sodium ions in solution},
	volume = {10},
	language = {en},
	number = {12},
	journal = {Biopolymers},
	author = {Frank-Kamenetskii, M. D.},
	month = dec,
	year = {1971},
	pages = {2623--2624},
}

@article{davis_thermodynamic_2008,
	title = {Thermodynamic characterization of naturally occurring {RNA} single mismatches with {G}-{U} nearest neighbors},
	volume = {47},
	number = {38},
	journal = {Biochemistry},
	author = {Davis, Amber R. and Znosko, Brent M.},
	month = sep,
	year = {2008},
	pages = {10178--10187},
}

@article{owczarzy_effects_2004,
	title = {Effects of sodium ions on {DNA} duplex oligomers: {Improved} predictions of melting temperatures},
	volume = {43},
	number = {12},
	journal = {Biochemistry},
	author = {Owczarzy, Richard and You, Yong and Moreira, Bernardo G. and Manthey, Jeffrey A. and Huang, Lingyan and Behlke, Mark A. and Walder, Joseph A.},
	month = mar,
	year = {2004},
	pages = {3537--3554},
}

@article{broda_thermodynamic_2005,
	title = {Thermodynamic stability of {RNA} structures formed by {CNG} trinucleotide repeats. {Implication} for prediction of {RNA} structure},
	volume = {44},
	number = {32},
	journal = {Biochemistry},
	author = {Broda, Magdalena and Kierzek, Elzbieta and Gdaniec, Zofia and Kulinski, Tadeusz and Kierzek, Ryszard},
	month = aug,
	year = {2005},
	pages = {10873--10882},
}

@article{hutton_renaturation_1977,
	title = {Renaturation kinetics and thermal stability of {DNA} in aqueous solutions of formamide and urea.},
	volume = {4},
	number = {10},
	journal = {Nucleic Acids Research},
	author = {Hutton, J R},
	month = oct,
	year = {1977},
	pages = {3537--3555},
}

@article{cullen_thermal_1976,
	title = {Thermal denaturation of {DNA} from bromodeoxyuridine substituted cells},
	volume = {3},
	number = {1},
	journal = {Nucleic Acids Research},
	author = {Cullen, Bryan R and Bick, Michael D},
	year = {1976},
	pages = {49--62},
}

@article{sugimoto_thermodynamic_1995,
	title = {Thermodynamic parameters to predict stability of {RNA}/{DNA} hybrid duplexes},
	volume = {34},
	number = {35},
	journal = {Biochemistry},
	author = {Sugimoto, Naoki and Nakano, Shu-ichi and Katoh, Misa and Matsumura, Akiko and Nakamuta, Hiroyuki and Ohmichi, Tatsuo and Yoneyama, Mari and Sasaki, Muneo},
	month = sep,
	year = {1995},
	pages = {11211--11216},
}

@article{sugimoto_improved_1996,
	title = {Improved thermodynamic parameters and helix initiation factor to predict stability of {DNA} duplexes.},
	volume = {24},
	number = {22},
	journal = {Nucleic Acids Research},
	author = {Sugimoto, N and Nakano, S and Yoneyama, M and Honda, K},
	month = nov,
	year = {1996},
	pages = {4501--4505},
}

@article{casey_rates_1977,
	title = {Rates of formation and thermal stabilities of {RNA}:{DNA} and {DNA}:{DNA} duplexes at high concentrations of formamide.},
	volume = {4},
	number = {5},
	journal = {Nucleic Acids Research},
	author = {Casey, J and Davidson, N},
	month = may,
	year = {1977},
	pages = {1539--1552},
}

@article{musielski_influence_1981,
	title = {Influence of dimethylsulfoxide on transcription by bacteriophage {T3}-induced {RNA} polymerase},
	volume = {21},
	number = {6},
	journal = {Zeitschrift fur allgemeine Mikrobiologie},
	author = {Musielski, H. and Mann, W. and Laue, R. and Michel, S.},
	year = {1981},
	pages = {447--456},
}

@article{kawakami_thermodynamic_2001,
	title = {Thermodynamic stability of base pairs between 2-hydroxyadenine and incoming nucleotides as a determinant of nucleotide incorporation specificity during replication},
	volume = {29},
	abstract = {We investigated the thermodynamic stability of double-stranded DNAs with an oxidative DNA lesion, 2-hydroxyadenine (2-OH-Ade),
in two different sequence contexts (5'-GA*C-3' and 5'-TA*A-3', A* represents 2-OH-Ade).
When an A*-N pair (N, any nucleotide base) was
located in the center of a duplex, the thermodynamic stabilities
of the duplexes were similar for all the natural bases except A
(N = T, C and G). On the other hand, for the duplexes with
the A*-N pair at the end, which mimic the nucleotide
incorporation step, the stabilities of the duplexes were dependent
on their sequence. The order of stability is T {>} G {>} C {>}{>} A
in the 5'-GA*C-3' sequences
and T {>} A {>} C {>} G in the 5'-TA*A-3' sequences. Because T/G/C
and T/A are nucleotides incorporated opposite to 2-OH-Ade
in the 5'-GA*C-3' and
5'-TA*A-3' sequences,
respectively, these results agree with the tendency of mutagenic
misincorporation of the nucleotides opposite to 2-OH-Ade in
vitro. Thus, the thermodynamic stability of the A*-N
base pair may be an important factor for the mutation spectra of
2-OH-Ade.},
	number = {16},
	journal = {Nucleic Acids Research},
	author = {Kawakami, Junji and Kamiya, Hiroyuki and Yasuda, Kyohko and Fujiki, Hiroyoshi and Kasai, Hiroshi and Sugimoto, Naoki},
	month = aug,
	year = {2001},
	pages = {3289--3296},
}

@article{watkins_nearest-neighbor_2005,
	title = {Nearest-neighbor thermodynamics of deoxyinosine pairs in {DNA} duplexes},
	volume = {33},
	number = {19},
	journal = {Nucleic Acids Research},
	author = {Watkins, Norman E and SantaLucia, John},
	month = jan,
	year = {2005},
	pages = {6258--6267},
}

@article{blake_thermal_1998,
	title = {Thermal stability of {DNA}},
	volume = {26},
	number = {14},
	journal = {Nucleic Acids Research},
	author = {Blake, R D and Delcourt, S G},
	month = jul,
	year = {1998},
	pages = {3323--3332},
}

@article{bommarito_thermodynamic_2000,
	title = {Thermodynamic parameters for {DNA} sequences with dangling ends},
	volume = {28},
	number = {9},
	journal = {Nucleic Acids Research},
	author = {Bommarito, Salvatore and Peyret, Nicolas and SantaLucia, John},
	month = may,
	year = {2000},
	pages = {1929--1934},
}

@article{allawi_thermodynamics_1998,
	title = {Thermodynamics of internal {C}\ifelse{html}{\out{&middot;}}{\eqn{\cdot}}{T} mismatches in {DNA}},
	volume = {26},
	number = {11},
	journal = {Nucleic Acids Research},
	author = {Allawi, Hatim T. and SantaLucia, John},
	year = {1998},
	pages = {2694--2701},
}

@incollection{blake_denaturation_1996,
	address = {Weinheim, Germany},
	title = {Denaturation of {DNA}},
	volume = {2},
	booktitle = {Encyclopedia of molecular biology and molecular medicine},
	publisher = {VCH Verlagsgesellschaft},
	author = {Blake, R. D.},
	editor = {Meyers, R. A.},
	year = {1996},
	pages = {1--19},
}

@article{asanuma_clear-cut_2005,
	title = {Clear-cut photo-regulation of the formation and dissociation of the {DNA} duplex by modified oligonucleotide involving multiple azobenzenes},
	language = {eng},
	number = {49},
	journal = {Nucleic Acids Symposium Series},
	author = {Asanuma, Hiroyuki and Matsunaga, Daijiro and Komiyama, Makoto},
	year = {2005},
	pmid = {17150620},
	pages = {35--36},
}

@article{mathews_expanded_1999,
	title = {Expanded sequence dependence of thermodynamic parameters improves prediction of {RNA} secondary structure},
	volume = {288},
	number = {5},
	journal = {Journal of Molecular Biology},
	author = {Mathews, David H. and Sabina, Jeffrey and Zuker, Michael and Turner, Douglas H.},
	month = may,
	year = {1999},
	pages = {911--940},
}

@article{marmur_determination_1962,
	title = {Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature},
	volume = {5},
	number = {1},
	journal = {Journal of Molecular Biology},
	author = {Marmur, J. and Doty, P.},
	month = jul,
	year = {1962},
	pages = {109--118},
}

@article{lu_set_2006,
	title = {A set of nearest neighbor parameters for predicting the enthalpy change of {RNA} secondary structure formation},
	volume = {34},
	number = {17},
	journal = {Nucleic Acids Research},
	author = {Lu, Zhi John and Turner, Douglas H and Mathews, David H},
	month = oct,
	year = {2006},
	pages = {4912--4924},
}

@article{kierzek_nearest_2006,
	title = {Nearest neighbor parameters for {Watson}-{Crick} complementary heteroduplexes formed between 2'-{O}-methyl {RNA} and {RNA} oligonucleotides},
	volume = {34},
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