Theoretical and Experimental Investigations of DNA Open States

A. S. Shigaev ; O. A. Ponomarev ; V. D. Lakhno

Matematičeskaâ biologiâ i bioinformatika, Tome 8 (2013), pp. 553-664.

Résumé

This research is a review and assay of literature data on the properties of DNA open states. The states result from large fluctuations of a duplex and have a great influence on a wide range of biochemical processes, including electric charge transfer in DNA. A comparative analysis of kinetic and thermodynamic experimental data on DNA open states has been performed for a wide temperature range. Apparent contradictions between the data of different experiments have been explained. Based on differences in thermodynamic properties and other characteristics three different types of DNA open states have been identified; a modern definition of the term "open state" has been given. A brief review of simple mathematical models of DNA has been presented; in most of the models the state of every base pair is defined by one or two variables. The central problems of investigation of heterogeneous DNA within the approaches of the level considered are examined. The roles of every model group in experimental data interpretation are discussed. Special emphasis is placed on the study of transfer and localization of base pair vibration energy in mechanical models. These processes have been shown to play a key role in heterogeneous duplex dynamics, and their theoretical treatment is critically important for the development of modern molecular biology and biophysics. The key features of theoretical approaches, that enabled description of various experimental data, have been considered. The future development of the models has been desribed, some particular details of their optimization have been suggested; probable ways of improving some experimental techniques have been proposed.

Bibliographie

[1] Alhambra C., Luque F. J., Gago F., Orozco M., “Ab Initio Study of Stacking Interactions in A- and B-DNA”, The Journal of Physical Chemistry B, 101 (1997), 3846–3853 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/jp962626a'>10.1021/jp962626a</ext-link>

[2] Hobza P., Sponer J., “Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations”, Chemical Reviews, 99 (1999), 3247–3276 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/cr9800255'>10.1021/cr9800255</ext-link>

[3] Sponer J., Leszczynski J., Hobza P., “Nature of Nucleic Acid-Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs”, The Journal of Physical Chemistry, 100 (1996), 5590–5596 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/jp953306e'>10.1021/jp953306e</ext-link>

[4] Tewari A. K., Dubey R., “Emerging trends in molecular recognition: utility of weak aromatic interactions”, Bioorganic & Medicinal Chemistry, 16 (2008), 126–143 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.bmc.2007.09.023'>10.1016/j.bmc.2007.09.023</ext-link>

[5] Watson D. G., Sutor D. J., Tollin P., “The crystal structure of deoxyadenosine monohydrate”, Acta Crystallographica, 19 (1965), 111–124 <ext-link ext-link-type='doi' href='https://doi.org/10.1107/S0365110X65002852'>10.1107/S0365110X65002852</ext-link>

[6] Kraut J., Jensen L. H., “Refinement of the crystal structure of adenosine-5'-phosphate”, Acta Crystallographica, 16 (1963), 79–88 <ext-link ext-link-type='doi' href='https://doi.org/10.1107/S0365110X63000207'>10.1107/S0365110X63000207</ext-link>

[7] Gago F., “Stacking Interactions and Intercalative DNA Binding”, Methods, 14 (1998), 277–292 <ext-link ext-link-type='doi' href='https://doi.org/10.1006/meth.1998.0584'>10.1006/meth.1998.0584</ext-link>

[8] Sponer J., Leszczynski J., Hobza P., “Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases”, Biopolymers, 61 (2001/2002), 3–31 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/1097-0282(2001)61:1&lt;3::AID-BIP10048&gt;3.0.CO;2-4'>10.1002/1097-0282(2001)61:1&lt;3::AID-BIP10048&gt;3.0.CO;2-4</ext-link>

[9] Cerny J., Hobza P., “Non-covalent interactions in biomacromolecules”, Physical Chemistry Chemical Physics, 9 (2007), 5291–5303 <ext-link ext-link-type='doi' href='https://doi.org/10.1039/b704781a'>10.1039/b704781a</ext-link>

[10] Nelson D., Koks M., Osnovy biokhimii Lenindzhera, Per. s angl., v 3 t., v. 1, BINOM. Laboratoriya znanii, M., 2011, 402 pp.

[11] Benham C. J., Mielke S. P., “DNA mechanics”, Annual Review of Biomedical Engineering, 7 (2005), 21–53 <ext-link ext-link-type='doi' href='https://doi.org/10.1146/annurev.bioeng.6.062403.132016'>10.1146/annurev.bioeng.6.062403.132016</ext-link>

[12] Vedenov A. A., Dykhne A. M., Frank-Kamenetskii M. D., “Perekhod spiral-klubok v DNK”, Uspekhi fizicheskikh nauk, 105:3 (1971), 479–519 <ext-link ext-link-type='doi' href='https://doi.org/10.3367/UFNr.0105.197111d.0479'>10.3367/UFNr.0105.197111d.0479</ext-link>

[13] Peyrard M., “Nonlinear dynamics and statistical physics of DNA”, Nonlinearity, 17 (2004), R1–R40 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/0951-7715/17/2/R01'>10.1088/0951-7715/17/2/R01</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2039047'>2039047</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1092.82015'>1092.82015</ext-link>

[14] Cloutier T., Widom J., “Spontaneous Sharp Bending of Double-Stranded DNA”, Molecular Cell, 14 (2004), 355–362 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S1097-2765(04)00210-2'>10.1016/S1097-2765(04)00210-2</ext-link>

[15] Yan J., Marko J. F., “Localized Single-Stranded Bubble Mechanism for Cyclization of Short Double Helix DNA”, Physical Review Letters, 93 (2004), 108108 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.93.108108'>10.1103/PhysRevLett.93.108108</ext-link>

[16] Cloutier T. E., Widom J., “DNA twisting flexibility and the formation of sharply looped protein-DNA complexes”, PNAS USA, 102 (2005), 3645–3650 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.0409059102'>10.1073/pnas.0409059102</ext-link>

[17] Du Q., Smith C., Shiffeldrim N., Vologodskaia M., Vologodskii A., “Cyclization of short DNA fragments and bending fluctuations of the double helix”, PNAS USA, 102 (2005), 5397–5402 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.0500983102'>10.1073/pnas.0500983102</ext-link>

[18] Feklistov A., Darst S. A., “Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit”, Cell, 147 (2011), 1257–1269 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.cell.2011.10.041'>10.1016/j.cell.2011.10.041</ext-link>

[19] Liu X., Bushnell D. A., Kornberg R. D., “Lock and key to transcription: sigma-DNA interaction”, Cell, 147 (2011), 1218–1219 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.cell.2011.11.033'>10.1016/j.cell.2011.11.033</ext-link>

[20] Eley D. D., Spivey D. I., “Semiconductivity of organic substances. 9: Nucleic acid in the dry state”, Transactions of the Faraday Society, 58 (1962), 411–415 <ext-link ext-link-type='doi' href='https://doi.org/10.1039/tf9625800411'>10.1039/tf9625800411</ext-link>

[21] Armitage B., “Photocleavage of Nucleic Acids”, Chemical Reviews, 98 (1998), 1171–1200 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/cr960428+'>10.1021/cr960428+</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1760206'>1760206</ext-link>

[22] Kino K., Sugiyama H., “Possible cause of G-C$\to$C-G transversion mutation by guanine oxidation product, imidazolone”, Chemistry & Biology, 8 (2001), 369–378 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S1074-5521(01)00019-9'>10.1016/S1074-5521(01)00019-9</ext-link>

[23] Wagenknecht H.-A., “Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics”, Natural Product Reports, 23 (2006), 973–1006 <ext-link ext-link-type='doi' href='https://doi.org/10.1039/b504754b'>10.1039/b504754b</ext-link>

[24] Kawanishi S., Hiraku Y., Oikawa S., “Mechanism of guanine-specific DNA damage by oxidative stress and its role in carcinogenesis and aging”, Mutation Research, 488 (2001), 65–76 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S1383-5742(00)00059-4'>10.1016/S1383-5742(00)00059-4</ext-link>

[25] Genereux J. C., Boal A. K., Barton J. K., “DNA-mediated Charge Transport in Redox Sensing and Signaling”, Journal of American Chemical Society, 132 (2010), 891–905 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja907669c'>10.1021/ja907669c</ext-link>

[26] Sontz P. A., Mui T. P., Fuss J. O., Tainer J. A., Barton J. K., “DNA charge transport as a first step in coordinating the detection of lesions by repair proteins”, PNAS USA, 109 (2012), 1856–1861 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.1120063109'>10.1073/pnas.1120063109</ext-link>

[27] Sontz P. A., Muren N. B., Barton J. K., “DNA Charge Transport for Sensing and Signaling”, Accounts of Chemical Research, 45 (2012), 1792–1800 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ar3001298'>10.1021/ar3001298</ext-link>

[28] Folta-Stogniew E., Russu I. M., “Sequence dependence of base-pair opening in a DNA dodecamer containing the CACA/GTGT sequence motif”, Biochemistry, 33 (1994), 11016–11024 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00202a022'>10.1021/bi00202a022</ext-link>

[29] Choi C. H., Kalosakas G., Rasmussen K. O., Hiromura M., Bishop A. R., Usheva A., “DNA dynamically directs its own transcription initiation”, Nucleic Acids Research, 32 (2004), 1584–1590 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkh335'>10.1093/nar/gkh335</ext-link>

[30] Kalosakas G., Rasmussen K. O., Bishop A. R., Choi C. H., Usheva A., “Sequence-specific thermal fluctuations identify start sites for DNA transcription”, Europhysics Letters, 68 (2004), 127–133 <ext-link ext-link-type='doi' href='https://doi.org/10.1209/epl/i2004-10167-8'>10.1209/epl/i2004-10167-8</ext-link>

[31] Lakhno V. D., “DNA Nanobioelectronics”, International Journal of Quantum Chemistry, 108 (2008), 1970–1981 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/qua.21717'>10.1002/qua.21717</ext-link>

[32] Triberis G. P., Dimakogianni M., “DNA in the material world: electrical properties and nano-applications”, Recent Patents on Nanotechnology, 3 (2009), 135–153 <ext-link ext-link-type='doi' href='https://doi.org/10.2174/187221009788490040'>10.2174/187221009788490040</ext-link>

[33] Hatfield G. W., Benham C. J., “DNA topology-mediated control of global gene expression in Escherichia coli”, Annual Review of Genetics, 36 (2002), 175–203 <ext-link ext-link-type='doi' href='https://doi.org/10.1146/annurev.genet.36.032902.111815'>10.1146/annurev.genet.36.032902.111815</ext-link>

[34] Mielke S. P., Gronbech-Jensen N. G., Krishnan V. V., Fink W. H., Benham C. J., “Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA”, The Journal of chemical physics, 123 (2005), 124911 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.2038767'>10.1063/1.2038767</ext-link>

[35] Zhabinskaya D., Benham C. J., “Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA”, PLoS Computational Biology, 7 (2011), e1001051 <ext-link ext-link-type='doi' href='https://doi.org/10.1371/journal.pcbi.1001051'>10.1371/journal.pcbi.1001051</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2776341'>2776341</ext-link>

[36] Watson J. D., Crick F. H., “Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid”, Nature, 171 (1953), 737–738 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/171737a0'>10.1038/171737a0</ext-link>

[37] Zimm B. H., Kallenbach N. R., “Selected Aspects of the Physical Chemistry of Polynucleotides and Nucleic Acids”, Annual Review of Physical Chemistry, 13 (1962), 171–194 <ext-link ext-link-type='doi' href='https://doi.org/10.1146/annurev.pc.13.100162.001131'>10.1146/annurev.pc.13.100162.001131</ext-link>

[38] Marmur J., Rownd R., Schildkraut C. L., “Denaturation and Renaturation of Deoxyribonucleic Acids”, Progress in Nucleic Acid Research and Molecular Biology, 1 (1963), 231–300 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0079-6603(08)60644-3'>10.1016/S0079-6603(08)60644-3</ext-link>

[39] Felsenfeld G., Miles H. T., “The Physical and Chemical Properties of Nucleic Acids”, Annual Review of Biochemistry, 36 (1967), 407–448 <ext-link ext-link-type='doi' href='https://doi.org/10.1146/annurev.bi.36.070167.002203'>10.1146/annurev.bi.36.070167.002203</ext-link>

[40] Thomas R., “Recherches sur la d'enaturation des acides desoxyribonucleiques”, Biochimica et Biophysica Acta, 14 (1954), 231–240 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0006-3002(54)90163-8'>10.1016/0006-3002(54)90163-8</ext-link>

[41] Rice S. A., Doty P., “The Thermal Denaturation of Deoxyribose Nucleic Acid”, Journal of American Chemical Society, 79 (1957), 3937–3947 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja01572a001'>10.1021/ja01572a001</ext-link>

[42] Zamenhof S., Alexander H. E., Leidy G., “Studies on the chemistry of the transforming activity. I: Resistance to physical and and chemical agents”, The Journal of Experimental Medicine, 98 (1953), 373–397 <ext-link ext-link-type='doi' href='https://doi.org/10.1084/jem.98.4.373'>10.1084/jem.98.4.373</ext-link>

[43] Bloomfield V. A., Crothers D. M., Tinoco I. Jr., Physical Chemistry of Nucleic acids, Harper & Row, New York, 1974, 133 pp.

[44] Tinoco I. Jr., “Hypochromism in Polynucleotides”, Journal of American Chemical Society, 82 (1960), 4785–4790 ; Erratum, Journal of American Chemical Society, 84 (1961), 5047 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja01503a007'>10.1021/ja01503a007</ext-link><ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja01485a643'>10.1021/ja01485a643</ext-link>

[45] Rhodes W., “Hypochromism and Other Spectral Properties of Helical Polynucleotides”, Journal of American Chemical Society, 83 (1961), 3609–3617 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja01478a017'>10.1021/ja01478a017</ext-link>

[46] De Voe H., “Optical Properties of Molecular Aggregates. I: Classical Model of Electronic Absorption and Refraction”, The Journal of chemical physics, 41:2 (1964), 393–400 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1725879'>10.1063/1.1725879</ext-link>

[47] Rhodes W., Chase M., “Generalized Susceptibility Theory. I: Theories of Hypochromism”, Reviews of Modern Physics, 39 (1967), 348–361 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/RevModPhys.39.348'>10.1103/RevModPhys.39.348</ext-link>

[48] Bullough R. K., “Complex Refractive Index and a Two-Band Model in the Theory of Hypochromism”, The Journal of chemical physics, 48 (1968), 3712–3722 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1669675'>10.1063/1.1669675</ext-link>

[49] De Voe H., “The theory of hypochromism of biopolymers: calculated spectra for DNA”, Annals of the New York Academy of Sciences, 158 (1969), 298–307 <ext-link ext-link-type='doi' href='https://doi.org/10.1111/j.1749-6632.1969.tb56227.x'>10.1111/j.1749-6632.1969.tb56227.x</ext-link>

[50] Brown E., Pysh E. S., “Base Composition Dependence of DNA Hypochromism”, The Journal of Chemical Physics, 56 (1972), 31–37 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1676865'>10.1063/1.1676865</ext-link>

[51] Volkov S. N., “Some aspects of the DNA hypochromic effect theory”, International Journal of Quantum Chemistry, 16:1 (1979), 119–132 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/qua.560160115'>10.1002/qua.560160115</ext-link>

[52] Russell A. P., Holleman D. S., “The thermal denaturation of DNA: average length and composition of denatured areas”, Nucleic Acids Research, 1 (1974), 959–978 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/1.8.959'>10.1093/nar/1.8.959</ext-link>

[53] Wartell R. M., Benight A. S., “Thermal denaturation of DNA molecules: A comparison of theory with experiment”, Physics Reports, 126 (1985), 67–107 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0370-1573(85)90060-2'>10.1016/0370-1573(85)90060-2</ext-link>

[54] Montrichok A., Gruner G., Zocchi G., “Trapping intermediates in the melting transition of DNA oligomers”, Europhysics Letters, 62 (2003), 452–458 <ext-link ext-link-type='doi' href='https://doi.org/10.1209/epl/i2003-00417-3'>10.1209/epl/i2003-00417-3</ext-link>

[55] Zeng Y., Montrichok A., Zocchi G., “Length and statistical weight of bubbles in DNA melting”, Physical Review Letters, 91 (2003), 148101 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.91.148101'>10.1103/PhysRevLett.91.148101</ext-link>

[56] Marmur J., Doty P., “Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature”, Journal of Molecular Biology, 5:1 (1962), 109–118 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2836(62)80066-7'>10.1016/S0022-2836(62)80066-7</ext-link>

[57] Nishigaki K., Husimi Y., Masuda M., Kaneko K., Tanaka T., “Strand dissociation and cooperative melting of double-stranded DNAs detected by denaturant gradient gel electrophoresis”, The Journal of Biochemistry, 95 (1984), 627–635

[58] Fodde R., Losekoot M., “Mutation detection by denaturing gradient gel electrophoresis (DGGE)”, Human mutation, 3 (1994), 83–94 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/humu.1380030202'>10.1002/humu.1380030202</ext-link>

[59] Wada A., Yabuki S., Husimi Y., “Fine structure in the thermal denaturation of DNA: high temperature-resolution spectrophotometric studies”, CRC critical reviews in biochemistry, 9 (1980), 87–144 <ext-link ext-link-type='doi' href='https://doi.org/10.3109/10409238009105432'>10.3109/10409238009105432</ext-link>

[60] Lazurkin Yu. S., Frank-Kamenetskii M. D., Trifonov E. N., “Melting of DNA: its study and application as a research method”, Biopolymers, 9 (1970), 1253–1306 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.1970.360091102'>10.1002/bip.1970.360091102</ext-link>

[61] Gotoh O., “Prediction of melting profiles and local helix stability for sequenced DNA”, Advances in Biophysics, 16 (1983), 1–52 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0065-227X(83)90007-2'>10.1016/0065-227X(83)90007-2</ext-link>

[62] Ivanov V., Zeng Y., Zocchi G., “Statistical mechanics of base stacking and pairing in DNA melting”, Physical Review E, 70 (2004), 051907 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.70.051907'>10.1103/PhysRevE.70.051907</ext-link>

[63] Rice S. A., Wada A., “On a model of the Helix-coil Transition in Macromolecules, II”, The Journal of Chemical Physics, 29 (1958), 233–243 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1744430'>10.1063/1.1744430</ext-link>

[64] Hill T. L., “Generalization of the One-Dimensional Ising Model Applicable to Helix Transitions in Nucleic Acids and Proteins”, The Journal of Chemical Physics, 30 (1959), 383–387 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1729961'>10.1063/1.1729961</ext-link>

[65] Zimm B. H., “Theory of “Melting” of the Helical Form in Double Chains of the DNA Type”, The Journal of Chemical Physics, 33 (1959), 1349–1356 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1731411'>10.1063/1.1731411</ext-link>

[66] Newell G. F., Montroll E. W., “On the Theory of the Ising Model of Ferromagnetism”, Reviews of Modern Physics, 25 (1953), 353–389 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/RevModPhys.25.353'>10.1103/RevModPhys.25.353</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=56511'>56511</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:0053.18601'>0053.18601</ext-link>

[67] Magee W. S. Jr., Gibbs J. H., Zimm B. H., “Theory of helix-coil transitions involving complementary poly- and oligo-nucleotides. I: The complete binding case”, Biopolymers, 1:2 (1963), 133–143 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.360010204'>10.1002/bip.360010204</ext-link>

[68] Magee W. S., Gibbs J. H., Newell G. F., “Statistical Thermodynamic Theory for Helix-Coil Transitions Involving Poly- and Oligonucleotides. II: The Case of Partial Binding”, The Journal of Chemical Physics, 43 (1965), 2115–2123 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1697082'>10.1063/1.1697082</ext-link>

[69] Schildkraut C., Lifson S., “Dependence of the melting temperature of DNA on salt concentration”, Biopolymers, 3:2 (1965), 195–208 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.360030207'>10.1002/bip.360030207</ext-link>

[70] Applequist J., Damle V., “Theory of the Effects of Concentration and Chain Length on Helix-Coil Equilibria in Two-Stranded Nucleic Acids”, The Journal of Chemical Physics, 39 (1963), 2719–2721 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1734089'>10.1063/1.1734089</ext-link>

[71] Poland D., Scheraga H. R., Theory of helix-coil transitions in biopolymers: statistical mechanical theory of order-disorder transitions in biological macromolecules, Acad. Press, New York, 1970, 797 pp.

[72] Crothers D. M., Kallenbach N. R., “On the Helix-Coil Transition in Heterogeneous Polymers”, The Journal of Chemical Physics, 45 (1966), 917–927 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1727704'>10.1063/1.1727704</ext-link>

[73] Lehman G. W., McTague J. P., “Melting of DNA”, The Journal of Chemical Physics, 49 (1968), 3170–3179 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1670566'>10.1063/1.1670566</ext-link>

[74] Brahms J., Maurizot J. C., Michelson A. M., “Conformational stability of dinucleotides in solution”, Journal of Molecular Biology, 25 (1967), 481–495 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(67)90200-8'>10.1016/0022-2836(67)90200-8</ext-link>

[75] Davis R. C., Tinoco I. Jr., “Temperature-dependent properties of dinucleoside phosphates”, Biopolymers, 6 (1968), 223–242 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.1968.360060206'>10.1002/bip.1968.360060206</ext-link>

[76] Inman R. B., Valdwin R. L., “Helix-Random Coil Transitions in DNA Homopolymer Pairs”, Journal of Molecular Biology, 8 (1964), 452–469 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2836(64)80003-6'>10.1016/S0022-2836(64)80003-6</ext-link>

[77] Shamberlin M. J., “Comparative properties of DNA, RNA, and hybrid homopolymer pairs”, Federation Proceedings, 24 (1965), 1446–1457

[78] Applequist J., “True Phase Transitions in Macromolecules of the DNA Type”, The Journal of Chemical Physics, 45 (1966), 3459–3461 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1728136'>10.1063/1.1728136</ext-link>

[79] Applequist J., “Higher-Order Phase Transitions in Two-Stranded Macromolecules”, The Journal of Chemical Physics, 50 (1969), 600–609 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1671105'>10.1063/1.1671105</ext-link>

[80] Landau L. D., Lifschitz E. M., Statistical Physics, Pergamon Press, Oxford, 1980, 387 pp. <ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=586944'>586944</ext-link>

[81] Mermin N., Wagner H., “Absence of ferro-magnetism or antiferromagnetism in one- or two-dimensional isotropic Heisenberg models”, Physical Review Letters, 17 (1966), 1133–1136 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.17.1133'>10.1103/PhysRevLett.17.1133</ext-link>

[82] Kac M., Uhlenbeck G. E., Hemmer P. C., “On the Van der Waals Theory of the Vapor-Liquid Equilibrium. I: Discussion of a One-Dimensional Model”, Journal of Mathematical Physics, 4 (1963), 216–228 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1703946'>10.1063/1.1703946</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=148416'>148416</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:0938.82517'>0938.82517</ext-link>

[83] Poland D., Scheraga H. A., “Phase transitions in one dimension and the helix-coil transition in polyamino acids”, The Journal of Chemical Physics, 45 (1966), 1456–1463 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1727785'>10.1063/1.1727785</ext-link>

[84] Poland D., Scheraga H. A., “Occurrence of a phase transition in nucleic acid models”, The Journal of Chemical Physics, 45 (1966), 1464–1469 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1727786'>10.1063/1.1727786</ext-link>

[85] Flory P. J., “Theory of Elastic Mechanisms in Fibrous Proteins”, Journal of American Chemical Society, 78 (1956), 5222–5235 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja01601a025'>10.1021/ja01601a025</ext-link>

[86] Fisher M. E., “Effect of Excluded Volume on Phase Transitions in Biopolymers”, The Journal of Chemical Physics, 45 (1966), 1469–1473 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1727787'>10.1063/1.1727787</ext-link>

[87] Lifshits I. M., Grosberg A. Yu., Khokhlov A. R., “Struktura polimernoi globuly, sformirovannoi nasyschayuschimisya svyazyami”, ZhETF, 71:4 (1976), 1634–1643

[88] Lifshits I. M., Grosberg A. Yu., Khokhlov A. R., “Ob'emnye vzaimodeistviya v statisticheskoi fizike polimernoi makromolekuly”, Uspekhi fizicheskikh nauk, 127:3 (1979), 353–389 <ext-link ext-link-type='doi' href='https://doi.org/10.3367/UFNr.0127.197903a.0353'>10.3367/UFNr.0127.197903a.0353</ext-link>

[89] Kuznetsov D. V., Khokhlov A. R., “Ob anomalnom perekhode klubok-globula v geteropolimernoi makromolekule”, Vysokomolekulyarnye soedineniya. Seriya B, 23B:1 (1981), 59–61

[90] Grosberg A. Yu., Khokhlov A. R., “Perekhody tipa klubok-globula v polimernykh sistemakh”, Problemy fiziki tverdogo tela, kurs lektsii, ed. Prokhorov A. M., Mir, M., 1984, 330–353

[91] Grosberg A. Yu., Khokhlov A. R., “Fazovye perekhody v polimernykh i biopolimernykh sistemakh”, Uspekhi fizicheskikh nauk, 149:4 (1986), 721–726

[92] Grosberg A. Yu., Khokhlov A. R., “After-Action of the Ideas of I. M. Lifshitz in Polymer and Biopolymer Physics”, Advances in Polymer Science, 196, Springer-Verlag, Berlin, 2006, 189–210 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/12_055'>10.1007/12_055</ext-link>

[93] Takahashi M., Yoshikawa K., Vasilevskaya V. V., Khokhlov A. R., “Discrete coil-globule transition of single duplex DNAs induced by polyamines”, The Journal of Physical Chemistry B, 101 (1997), 9396–9401 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/jp9716391'>10.1021/jp9716391</ext-link>

[94] Mukherji S., Bhattacharjee S. M., “Directed polymers with random interaction: An exactly solvable case”, Physical Review E, 48 (1993), 3483–3496 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.48.3483'>10.1103/PhysRevE.48.3483</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1376966'>1376966</ext-link>

[95] Bhattacharjee S. M., Mukherji S., “Directed polymers with random interaction: Marginal relevance and novel criticality”, Physical Review Letters, 70 (1993), 49–52 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.70.49'>10.1103/PhysRevLett.70.49</ext-link>

[96] Causo M. S., Coluzzi B., Grassberger P., “Simple model for the DNA denaturation transition”, Physical Review E, 62 (2000), 3958–3973 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.62.3958'>10.1103/PhysRevE.62.3958</ext-link>

[97] Kafri Y., Mukamel D., Peliti L., Why is the DNA Denaturation Transition First Order?, Physical Review Letters, 85 (2000), 4988–4991 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.85.4988'>10.1103/PhysRevLett.85.4988</ext-link>

[98] Duplantier B., “Polymer Network of fixed topology: renormalization, exact critical exponent $\gamma$ in two dimensions, and $d=4-\varepsilon$”, Physical Review Letters, 57 (1986), 941–944 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.57.941'>10.1103/PhysRevLett.57.941</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=853268'>853268</ext-link>

[99] Duplantier B., “Statistical Mechanics of Polymer Networks”, Journal of Statistical Physics, 54 (1989), 581–680 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/BF01019770'>10.1007/BF01019770</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=988554'>988554</ext-link>

[100] Schafer L., von Ferber C., Lehr U., Duplantier B., “Renormalization of polymer networks and stars”, Nuclear Physics B, 374 (1992), 473–495 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0550-3213(92)90397-T'>10.1016/0550-3213(92)90397-T</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1162692'>1162692</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:0992.82511'>0992.82511</ext-link>

[101] Garel T., Monthus C., Orland H., “A simple model for DNA denaturation”, Europhysics Letters, 55 (2001), 132–138 <ext-link ext-link-type='doi' href='https://doi.org/10.1209/epl/i2001-00391-2'>10.1209/epl/i2001-00391-2</ext-link>

[102] Carlon E., Orlandini E., Stella A. L., “Roles of Stiffness and Excluded Volume in DNA Denaturation”, Physical Review Letters, 88 (2002), 198101 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.88.198101'>10.1103/PhysRevLett.88.198101</ext-link>

[103] Baiesi M., Carlon E., Stella A. L., “Scaling in DNA unzipping models: Denaturated loops and end segments as branches of a block copolymer network”, Physical Review E, 66 (2002), 021804 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.66.021804'>10.1103/PhysRevE.66.021804</ext-link>

[104] Blossey R., Carlon E., “Reparametrizing the loop entropy weights: Effect on DNA melting curves”, Physical Review E, 68 (2003), 061911 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.68.061911'>10.1103/PhysRevE.68.061911</ext-link>

[105] Baiesi M., Carlon E., Kafri Y., Mukamel D., Orlandini E., Stella A. L., “Interstrand distance distribution of DNA near melting”, Physical Review E, 67 (2003), 021911 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.67.021911'>10.1103/PhysRevE.67.021911</ext-link>

[106] Garel T., Monthus C., “Numerical study of the disordered Poland–Scheraga model of DNA denaturation”, Journal of Statistical Mechanics: Theory and Experiment, 2005 (2005), P06004 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/1742-5468/2005/06/P06004'>10.1088/1742-5468/2005/06/P06004</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2166541'>2166541</ext-link>

[107] Coluzzi B., “Numerical study of a disordered model for DNA denaturation transition”, Physical Review E, 73 (2006), 011911 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.73.011911'>10.1103/PhysRevE.73.011911</ext-link>

[108] Coluzzi B., Yeramian E., “Numerical evidence for relevance of disorder in a Poland–Scheraga DNA denaturation model with self-avoidance: scaling behavior of average quantities”, The European Physical Journal B, 56 (2007), 349–365 <ext-link ext-link-type='doi' href='https://doi.org/10.1140/epjb/e2007-00140-5'>10.1140/epjb/e2007-00140-5</ext-link>

[109] Bar A., Kafri Y., Mukamel D., “Loop Dynamics in DNA Denaturation”, Physical Review Letters, 98 (2007), 038103 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.98.038103'>10.1103/PhysRevLett.98.038103</ext-link>

[110] Kunz H., Livi R., Suto A., “The structure factor and dynamics of the helix-coil transition”, Journal of Statistical Mechanics: Theory and Experiment, 2007 (2007), P06004 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/1742-5468/2007/06/P06004'>10.1088/1742-5468/2007/06/P06004</ext-link>

[111] Bandyopadhyay M., Gupta S., Segal D., “DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals”, Physical Review E, 83 (2011), 031905 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.83.031905'>10.1103/PhysRevE.83.031905</ext-link>

[112] Inman R. B., “A denaturation map of the lambda phage DNA molecule determined by electron microscopy”, Journal of Molecular Biology, 18 (1966), 464–476 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2836(66)80037-2'>10.1016/S0022-2836(66)80037-2</ext-link>

[113] Hirschman S. Z., Gellert M., Falkow S., Felsenfeld G., “Spectral analysis of the intramolecular heterogeneity of lambda DNA”, Journal of Molecular Biology, 28 (1967), 469–477 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2836(67)80097-4'>10.1016/S0022-2836(67)80097-4</ext-link>

[114] Sanger F., Coulson A. R., Hong G. F., Hill D. F., Petersen G. B., “Nucleotide sequence of bacteriophage lambda DNA”, Journal of Molecular Biology, 162 (1982), 729–773 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(82)90546-0'>10.1016/0022-2836(82)90546-0</ext-link>

[115] Falkow S., Cowie D. B., “Intramolecular heterogeneity of the deoxyribonucleic acid of temperate bacteriophages”, Journal of Bacteriology, 96 (1968), 777–784

[116] Hanlon S., Johnson R. S., Wolf B., Chan A., “Mixed Conformations of Deoxyribonucleic Acid in Chromatin: A Preliminary Report”, PNAS USA, 69 (1972), 3263–3267 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.69.11.3263'>10.1073/pnas.69.11.3263</ext-link>

[117] Tashiro T., Kurokawa M., “A Contribution of Nonhistone Proteins to the Conformation of Chromatin”, European Journal of Biochemistry, 60 (1975), 569–577 <ext-link ext-link-type='doi' href='https://doi.org/10.1111/j.1432-1033.1975.tb21035.x'>10.1111/j.1432-1033.1975.tb21035.x</ext-link>

[118] Darzynkiewicz Z., Traganos F., Sharpless T., Melamed M. R., “DNA denaturation in situ. Effect of divalent cations and alcohols”, The Journal of Cell Biology, 68 (1976), 1–10 <ext-link ext-link-type='doi' href='https://doi.org/10.1083/jcb.68.1.1'>10.1083/jcb.68.1.1</ext-link>

[119] Defert N., Kitzist A., Kruht J., Brahms S., Brahms J., “Effect of non-histone proteins on thermal transition of chromatin and of DNA”, Nucleic Acids Research, 4 (1977), 2293–2306 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/4.7.2293'>10.1093/nar/4.7.2293</ext-link>

[120] Li H. J., Brand B., Rotter A., “Thermal denaturation of calf thymus DNA: existence of a GC-richer fraction”, Nucleic Acids Research, 1 (1974), 257–265 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/1.2.257'>10.1093/nar/1.2.257</ext-link>

[121] Fonty G., Crouse E. J., Stutz E., Bernard G., “The Mitochondrial Genome of Euglena gracilis”, European Journal of Biochemistry, 54 (1975), 367–372 <ext-link ext-link-type='doi' href='https://doi.org/10.1111/j.1432-1033.1975.tb04147.x'>10.1111/j.1432-1033.1975.tb04147.x</ext-link>

[122] Schmitt J. M., Bonhert H.-J., Gordon K. H. J., Herrmann R., Bernardi G., Crouse E. J., “Compositional Heterogeneity of the Chloroplast DNAs from Euglena gracilis and Spinacia oleracea”, European Journal of Biochemistry, 117 (1981), 375–382 <ext-link ext-link-type='doi' href='https://doi.org/10.1111/j.1432-1033.1981.tb06348.x'>10.1111/j.1432-1033.1981.tb06348.x</ext-link>

[123] Lyon E., “Mutation detection using fluorescent hybridization probes and melting curve analysis”, Expert Review of Molecular Diagnostics, 1 (2001), 92–101 <ext-link ext-link-type='doi' href='https://doi.org/10.1586/14737159.1.1.92'>10.1586/14737159.1.1.92</ext-link>

[124] Ruskova L., Raclavsky V., “The potential of high resolution melting analysis (HRMA) to streamline, facilitate and enrich routine diagnostics in medical microbiology”, Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia, 155, 2011, 239–252 <ext-link ext-link-type='doi' href='https://doi.org/10.5507/bp.2011.045'>10.5507/bp.2011.045</ext-link>

[125] Li B. S., Wang X. Y., Ma F. L., Jiang B., Song X. X., Xu A. G., “Is high resolution melting analysis (HRMA) accurate for detection of human disease-associated mutations? A meta analysis”, PLoS One, 6 (2011), e28078 <ext-link ext-link-type='doi' href='https://doi.org/10.1371/journal.pone.0028078'>10.1371/journal.pone.0028078</ext-link>

[126] Vossen R. H., Aten E., Roos A., den Dunnen J. T., “High-resolution melting analysis (HRMA): more than just sequence variant screening”, Human Mutation, 30 (2009), 860–866 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/humu.21019'>10.1002/humu.21019</ext-link>

[127] Ghorashi S. A., Noormohammadi A. H., Markham P. F., “Differentiation of Mycoplasma gallisepticum strains using PCR and high-resolution melting curve analysis”, Microbiology, 156 (2010), 1019–1029 <ext-link ext-link-type='doi' href='https://doi.org/10.1099/mic.0.031351-0'>10.1099/mic.0.031351-0</ext-link>

[128] Lyamichev V. I., Panyutin I. G., Cherny D. I., Lyubchenko Yu. L., “Localization of low-melting regions in phage T7 DNA”, Nucleic Acids Research, 11 (1983), 2165–2176 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/11.7.2165'>10.1093/nar/11.7.2165</ext-link>

[129] Wartell R. M., Benight A. S., “Fluctuational Base-Pair Opening in DNA at Temperatures Below the Helix-Coil Transition Region”, Biopolymers, 21 (1982), 2069–2081 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.360211011'>10.1002/bip.360211011</ext-link>

[130] Steger G., “Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction”, Nucleic Acids Research, 22 (1994), 2760–2768 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/22.14.2760'>10.1093/nar/22.14.2760</ext-link>

[131] Blake R. D., Bizzaro J. W., Blake J. D., Day G. R., Delcourt S. G., Knowles J., Marx K. A., Santa-Lucia J. Jr., “Statistical mechanical simulation of polymeric DNA melting with MELTSIM”, Bioinformatics, 15 (1999), 370–375 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/bioinformatics/15.5.370'>10.1093/bioinformatics/15.5.370</ext-link>

[132] Rasmussen J. P., Saint C. P., Monis P. T., “Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes”, BMC Bioinformatics, 8 (2007), 107 <ext-link ext-link-type='doi' href='https://doi.org/10.1186/1471-2105-8-107'>10.1186/1471-2105-8-107</ext-link>

[133] Yeramian E., Jones L., “GeneFizz: A web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives”, Nucleic Acids Research, 31 (2003), 3843–3849 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkg627'>10.1093/nar/gkg627</ext-link>

[134] Leber M., Kaderali L., Schonhuth A., Schrader R., “A fractional programming approach to efficient DNA melting temperature calculation”, Bioinformatics, 21 (2005), 2375–2382 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/bioinformatics/bti379'>10.1093/bioinformatics/bti379</ext-link>

[135] Yeramian E., “Genes and the physics of the DNA double-helix”, Gene, 255 (2000), 139–150 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0378-1119(00)00301-2'>10.1016/S0378-1119(00)00301-2</ext-link>

[136] Yeramian E., “The physics of DNA and the annotation of the Plasmodium falciparum genome”, Gene, 255 (2000), 151–168 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0378-1119(00)00300-0'>10.1016/S0378-1119(00)00300-0</ext-link>

[137] Gaeta G., Reiss C., Peyrard M., Dauxois T., “Simple models of non-linear DNA dynamics”, La Rivista del Nuovo Cimento, Ser. 3, 17:4 (1994), 1–48 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/BF02724511'>10.1007/BF02724511</ext-link>

[138] Yakushevich L. V., Nonlinear Physics of DNA, 2nd Edition, Wiley, New York, 2004, 207 pp.

[139] Mandal C., Kallenbach N. R., Englander S. W., “Base-pair opening and closing reactions in the double helix: A stopped-flow hydrogen exchange study in poly(rA):poly(rU)”, Journal of Molecular Biology, 135 (1979), 391–411 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(79)90443-1'>10.1016/0022-2836(79)90443-1</ext-link>

[140] Englander S. W., Kallenbach N. R., Heeger A. J., Krumhansl J. A., Litwin S., “Nature of the open state in long polynucleotide double helices: possibility of soliton excitations”, PNAS USA, 77 (1980), 7222–7226 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.77.12.7222'>10.1073/pnas.77.12.7222</ext-link>

[141] Yomosa S., “Soliton excitations in deoxyribonucleic acid (DNA) double helices”, Physical Review A, 27 (1983), 2120–2125 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.27.2120'>10.1103/PhysRevA.27.2120</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=700064'>700064</ext-link>

[142] Yomosa S., “Solitary excitations in deoxyribonucleic acid (DNA) double helices”, Physical Review A, 30 (1984), 474–480 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.30.474'>10.1103/PhysRevA.30.474</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=700064'>700064</ext-link>

[143] Teitelbaum H., Englander S. W., “Open states in native polynucleotides. I: Hydrogen-exchange study of adenine-containing double helices”, Journal of Molecular Biology, 92 (1975), 55–78 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(75)90091-1'>10.1016/0022-2836(75)90091-1</ext-link>

[144] Teitelbaum H., Englander S. W., “Open states in native polynucleotides. II: Hydrogen-exchange study of cytosine-containing double helices”, Journal of Molecular Biology, 92 (1975), 79–92 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(75)90092-3'>10.1016/0022-2836(75)90092-3</ext-link>

[145] Nakanishi M., Tsuboi M., “Two channels of hydrogen exchange in a double-helical nucleic acid”, Journal of Molecular Biology, 124 (1978), 61–71 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(78)90147-X'>10.1016/0022-2836(78)90147-X</ext-link>

[146] Takeno S., Homma S., “Topological Solitons and Modulated Structure of Bases in DNA Double Helices — A Dynamic Plane Base-Rotator Model”, Progress of Theoretical Physics, 70 (1983), 308–311 <ext-link ext-link-type='doi' href='https://doi.org/10.1143/PTP.70.308'>10.1143/PTP.70.308</ext-link>

[147] Homma S., Takeno S., “A Coupled Base-Rotator Model for Structure and Dynamics of DNA — Local Fluctuations in Helical Twist Angles and Topological Solitons”, Progress of Theoretical Physics, 72 (1984), 679–693 <ext-link ext-link-type='doi' href='https://doi.org/10.1143/PTP.72.679'>10.1143/PTP.72.679</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=772719'>772719</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1074.92501'>1074.92501</ext-link>

[148] Zhang C.-T., “Soliton excitations in deoxyribonucleic acid (DNA) double helices”, Physical Review A, 35 (1987), 886–891 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.35.886'>10.1103/PhysRevA.35.886</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=870770'>870770</ext-link>

[149] Gao Y., Prohofsky E. W., “A modified self-consistent phonon theory of hydrogen bond melting”, The Journal of Chemical Physics, 80 (1984), 2242 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.446921'>10.1063/1.446921</ext-link>

[150] Gao Y., Devi-Prasad K. V., Prohofsky E. W., “A self-consistent microscopic theory of hydrogen bond melting with application to poly(dG)-poly(dC)”, The Journal of Chemical Physics, 80 (1984), 6291 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.446732'>10.1063/1.446732</ext-link>

[151] Prohofsky E. W., “Solitons hiding in DNA and their possible significance in RNA transcription”, Physical Review A, 38 (1988), 1538–1541 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.38.1538'>10.1103/PhysRevA.38.1538</ext-link>

[152] Peyrard M., Bishop A. R., “Statistical Mechanics of a Nonlinear Model for DNA Denaturation”, Physical Review Letters, 62 (1989), 2755–2758 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.62.2755'>10.1103/PhysRevLett.62.2755</ext-link>

[153] Dauxois T., Peyrard M., Bishop A. R., “Dynamics and thermodynamics of a nonlinear model for DNA denaturation”, Physical Review E, 47 (1993), 684–695 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.47.684'>10.1103/PhysRevE.47.684</ext-link>

[154] Dauxois T., Peyrard M., Bishop A. R., “Entropy-driven DNA denaturation”, Physical Review E, 47 (1993), R44–R47 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.47.R44'>10.1103/PhysRevE.47.R44</ext-link>

[155] Cule D., Hwa T., “Denaturation of Heterogeneous DNA”, Physical Review Letters, 79 (1997), 2375–2378 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.79.2375'>10.1103/PhysRevLett.79.2375</ext-link>

[156] Dauxois T., Peyrard M., “Entropy-driven transition in a one-dimensional system”, Physical Review E, 51 (1995), 4027–4040 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.51.4027'>10.1103/PhysRevE.51.4027</ext-link>

[157] Van Zandt L. L., “DNA solitons with realistic parameter values”, Physical Review A, 40 (1989), 6134–6137 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.40.6134'>10.1103/PhysRevA.40.6134</ext-link>

[158] Techera M., Daemen L. L., Prohofsky E. W., “Comment on “DNA solitons with realistic parameters””, Physical Review A, 42 (1990), 5033–5035 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.42.5033'>10.1103/PhysRevA.42.5033</ext-link>

[159] Van Zandt L. L., “Reply to “Comment on `DNA solitons with realistic parameters””, Physical Review A, 42 (1990), 5036–5039 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.42.5036'>10.1103/PhysRevA.42.5036</ext-link>

[160] Drigo-Filho E., Ruggiero J. R., “Parameters describing the H-bond in DNA”, Physical Review A, 44 (1991), 8435–8436 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.44.8435'>10.1103/PhysRevA.44.8435</ext-link>

[161] Banavali N. K., MacKerell A. D. Jr., “Free energy and structural pathways of base flipping in a DNA GCGC containing sequence”, Journal of Molecular Biology, 319 (2002), 141–160 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2836(02)00194-8'>10.1016/S0022-2836(02)00194-8</ext-link>

[162] Giudice E., Varnai P., Lavery R., “Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations”, Nucleic Acids Research, 31 (2003), 1434–1443 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkg239'>10.1093/nar/gkg239</ext-link>

[163] Bouvier B., Grubmuller H., “A Molecular Dynamics Study of Slow Base Flipping in DNA using Conformational Flooding”, Biophysical Journal, 93 (2007), 770–786 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.106.091751'>10.1529/biophysj.106.091751</ext-link>

[164] Yakushevich L. V., “Nonlinear DNA dynamics: a new model”, Physics Letters A, 136 (1989), 413–417 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0375-9601(89)90425-8'>10.1016/0375-9601(89)90425-8</ext-link>

[165] Yakushevich L. V., Is DNA a nonlinear dynamical system where solitary conformational waves are possible?, Journal of Biosciences, 26 (2001), 305–313 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/BF02703739'>10.1007/BF02703739</ext-link>

[166] Yakushevich L. V., “Modeling the Internal Mobility of the Molecule of DNA”, International Journal of Quantum Chemistry, 88 (2002), 570–578 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/qua.10209'>10.1002/qua.10209</ext-link>

[167] Yakushevich L. V., Savin A. V., Manevitch L. I., “Nonlinear dynamics of topological solitons in DNA”, Physical Review E, 66 (2002), 016614 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.66.016614'>10.1103/PhysRevE.66.016614</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1919757'>1919757</ext-link>

[168] Gaeta G., “Solitons in the Yakushevich model of DNA beyond the contact approximation”, Physical Review E, 74 (2006), 021921 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.74.021921'>10.1103/PhysRevE.74.021921</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2280413'>2280413</ext-link>

[169] Cadoni M., De Leo R., Gaeta G., “Composite model for DNA torsion dynamics”, Physical Review E, 75 (2007), 021919 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.75.021919'>10.1103/PhysRevE.75.021919</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2354022'>2354022</ext-link>

[170] Daniel M., Vasumathi V., “Solitonlike base pair opening in a helicoidal DNA: An analogy with a helimagnet and a cholesteric liquid crystal”, Physical Review E, 79 (2009), 012901 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.79.012901'>10.1103/PhysRevE.79.012901</ext-link>

[171] Cadoni M., De Leo R., Demelio S., “Soliton propagation in homogeneous and non-homogeneous models for DNA torsion dynamics”, Journal of Nonlinear Mathematical Physics, 18 (2011), 287–319 <ext-link ext-link-type='doi' href='https://doi.org/10.1142/S1402925111001544'>10.1142/S1402925111001544</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2827504'>2827504</ext-link>

[172] Yakushevich L. V., Ryasik A. A., “Dinamicheskie kharakteristiki kinkov i antikinkov DNK”, Kompyuternye issledovaniya i modelirovanie, 4:1 (2012), 209–217

[173] Barbi M., Cocco S., Peyrard M., “Helicoidal model for DNA opening”, Physics Letters A, 253 (1999), 358–369 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0375-9601(99)00059-6'>10.1016/S0375-9601(99)00059-6</ext-link>

[174] Barbi M., Cocco S., Peyrard M., Ruffo S., “A Twist Opening Model for DNA”, Journal of Biological Physics, 24 (1999), 97–114 <ext-link ext-link-type='doi' href='https://doi.org/10.1023/A:1005139326775'>10.1023/A:1005139326775</ext-link>

[175] Campa A., “Bubble propagation in a helicoidal molecular chain”, Physical Review E, 63 (2001), 021901 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.63.021901'>10.1103/PhysRevE.63.021901</ext-link>

[176] Cocco S., Monasson R., “Statistical Mechanics of Torque Induced Denaturation of DNA”, Physical Review Letters, 83 (1999), 5178–5181 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.83.5178'>10.1103/PhysRevLett.83.5178</ext-link>

[177] Cocco S., Monasson R., “Theoretical study of collective modes in DNA at ambient temperature”, The Journal of Chemical Physics, 112 (2000), 10017–10033 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.481646'>10.1063/1.481646</ext-link>

[178] Cocco S., Monasson R., Marko J. F., “Force and kinetic barriers to initiation of DNA unzipping”, Physical Review E, 65 (2002), 041907 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.65.041907'>10.1103/PhysRevE.65.041907</ext-link>

[179] Barbi M., Lepri S., Peyrard M., Theodorakopoulos N., “Thermal denaturation of a helicoidal DNA model”, Physical Review E, 68 (2003), 061909 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.68.061909'>10.1103/PhysRevE.68.061909</ext-link>

[180] Cocco S., Monasson R., Marko J. F., “Force and kinetic barriers to unzipping of the DNA double helix”, PNAS USA, 98 (2001), 8608–8613 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.151257598'>10.1073/pnas.151257598</ext-link>

[181] Drukker K., Wu G., Schatz G. C., “Model simulations of DNA denaturation dynamics”, Journal of Chemical Physics, 114 (2001), 579–590 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1329137'>10.1063/1.1329137</ext-link>

[182] Calvo G. F., Alvarez-Estrada R. F., “Three-dimensional models for homogeneous DNA near denaturation”, Journal of Physics: Condensed Matter, 17 (2005), 7755–7781 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/0953-8984/17/50/001'>10.1088/0953-8984/17/50/001</ext-link>

[183] Hien D. L., Nhan N. T., Thanh Ngo V., Viet N. A., “Simple combined model for nonlinear excitations in DNA”, Physical Review E, 76 (2007), 021921 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.76.021921'>10.1103/PhysRevE.76.021921</ext-link>

[184] Goldman C., Olson W. K., “DNA denaturation as a problem of translational-symmetry restoration”, Physical Review E, 48 (1993), 1461–1468 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.48.1461'>10.1103/PhysRevE.48.1461</ext-link>

[185] Pitici F., Svirschevski S., “Effective-phonon theory for DNA melting”, Physical Review A, 44 (1991), 8348–8355 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.44.8348'>10.1103/PhysRevA.44.8348</ext-link>

[186] Zoli M., “Path integral method for DNA denaturation”, Physical Review E, 79 (2009), 041927 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.79.041927'>10.1103/PhysRevE.79.041927</ext-link>

[187] Ares S., Sanchez A., “Modelling disorder: the cases of wetting and DNA denaturation”, European Physical Journal B, 56 (2007), 253–258 <ext-link ext-link-type='doi' href='https://doi.org/10.1140/epjb/e2007-00112-9'>10.1140/epjb/e2007-00112-9</ext-link>

[188] Theodorakopoulos N., Dauxois T., Peyrard M., “Order of the Phase Transition in Models of DNA Thermal Denaturation”, Physical Review Letters, 85 (2000), 6–9 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.85.6'>10.1103/PhysRevLett.85.6</ext-link>

[189] Zhang Y., Zheng W.-M., Liu J.-X., Chen Y. Z., “Theory of DNA melting based on the Peyrard–Bishop model”, Physical Review E, 56 (1997), 7100–7115 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.56.7100'>10.1103/PhysRevE.56.7100</ext-link>

[190] Joyeux M., Buyukdagli S., “Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation”, Physical Review E, 72 (2005), 051902 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.72.051902'>10.1103/PhysRevE.72.051902</ext-link>

[191] Buyukdagli S., Sanrey M., Joyeux M., “Towards more realistic dynamical models for DNA secondary structure”, Chemical Physics Letters, 419 (2006), 434–438 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.cplett.2005.12.009'>10.1016/j.cplett.2005.12.009</ext-link>

[192] Radosz A., Ostasiewicz K., Magnuszewski P., Damczyk J., Radosinski L., Kusmartsev F. V., Samson J. H., Mitus A. C., Pawlik G., “Thermodynamics of entropy-driven phase transformations”, Physical Review E, 73 (2006), 026127 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.73.026127'>10.1103/PhysRevE.73.026127</ext-link>

[193] Weber G., “Sharp DNA denaturation due to solvent interaction”, Europhysics Letters, 73 (2006), 806–811 <ext-link ext-link-type='doi' href='https://doi.org/10.1209/epl/i2005-10466-6'>10.1209/epl/i2005-10466-6</ext-link>

[194] Cuenda S., Sanchez A., “On the discrete Peyrard-Bishop model of DNA: Stationary solutions and stability”, CHAOS, 16 (2006), 023123 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.2194468'>10.1063/1.2194468</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1146.37314'>1146.37314</ext-link>

[195] Zamora-Sillero E., Shapovalov A. V., Esteban F. J., “Formation, control, and dynamics of N localized structures in the Peyrard–Bishop model”, Physical Review E, 76 (2007), 066603 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.76.066603'>10.1103/PhysRevE.76.066603</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2365623'>2365623</ext-link>

[196] Slade G. G., Drigo Filho E., Ruggiero J. R., “Stability of breathers in simple mechanical models for DNA”, Journal of Physics: Conference Series, 246 (2010), 012039 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/1742-6596/246/1/012039'>10.1088/1742-6596/246/1/012039</ext-link>

[197] Tabi C. B., Ekobena Fouda H. P., Mohamadou A., Kofane T. C., “Wave propagation of coupled modes in the DNA double helix”, Physica Scripta, 83 (2011), 035802 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/0031-8949/83/03/035802'>10.1088/0031-8949/83/03/035802</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1218.92011'>1218.92011</ext-link>

[198] Tabi C. B., Mohamadou A., Kofane T. C., “Soliton excitation in the DNA double helix”, Physica Scripta, 77 (2008), 045002 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/0031-8949/77/4/045002'>10.1088/0031-8949/77/4/045002</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1136.92306'>1136.92306</ext-link>

[199] Tabi C. B., Mohamadou A., Kofane T. C., “Modulational instability in the anharmonic Peyrard–Bishop model of DNA”, European Physical Journal B, 74 (2010), 151–158 <ext-link ext-link-type='doi' href='https://doi.org/10.1140/epjb/e2010-00062-1'>10.1140/epjb/e2010-00062-1</ext-link>

[200] Maniadis P., Alexandrov B. S., Bishop A. R., Rasmussen K. O., “Feigenbaum cascade of discrete breathers in a model of DNA”, Physical Review E, 83 (2011), 011904 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.83.011904'>10.1103/PhysRevE.83.011904</ext-link>

[201] Zdravkovic S., Sataric M. V., “The Impact of Viscosity on the DNA Dynamics”, Physica Scripta, 64 (2001), 612–619 <ext-link ext-link-type='doi' href='https://doi.org/10.1238/Physica.Regular.064a00612'>10.1238/Physica.Regular.064a00612</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1060.92011'>1060.92011</ext-link>

[202] Zdravkovic S., Sataric M. V., “Solitonic speed in DNA”, Physical Review E, 77 (2008), 031906 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.77.031906'>10.1103/PhysRevE.77.031906</ext-link>

[203] Cuevas J., Archilla J. F. R., Gaididei Yu. B., Romero F. R., “Moving breathers in a DNA model with competing short- and long-range dispersive interactions”, Physica D: Nonlinear Phenomena, 163 (2002), 106–126 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0167-2789(02)00351-2'>10.1016/S0167-2789(02)00351-2</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1887045'>1887045</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1001.92007'>1001.92007</ext-link>

[204] Larsen P. V., Christiansen P. L., Bang O., Archilla J. F. R., Gaididei Yu. B., “Energy funneling in a bent chain of Morse oscillators with long-range coupling”, Physical Review E, 69 (2004), 026603 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.69.026603'>10.1103/PhysRevE.69.026603</ext-link>

[205] Alvarez A., Romero F. R., Archilla J. F. R., Cuevas J., Larsen P. V., “Breather trapping and breather transmission in a DNA model with an interface”, European Physical Journal B, 51 (2006), 119–130 <ext-link ext-link-type='doi' href='https://doi.org/10.1140/epjb/e2006-00191-0'>10.1140/epjb/e2006-00191-0</ext-link>

[206] Forinash K., Keeney J., “Nonlinearly coupled double chain systems”, Journal of Biological Physics, 18 (1991), 19–29 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/BF00383787'>10.1007/BF00383787</ext-link>

[207] Alvarez A., Romero F. R., Cuevas J., Archilla J. F. R., “Moving breather collisions in Klein–Gordon chains of oscillators”, European Physical Journal B, 70 (2009), 543–555 <ext-link ext-link-type='doi' href='https://doi.org/10.1140/epjb/e2009-00256-6'>10.1140/epjb/e2009-00256-6</ext-link>

[208] Wattis J. A. D., Harris S. A., Grindon C. R., Laughton C. A., “Dynamic model of base pair breathing in a DNA chain with a defect”, Physical Review E, 63 (2001), 061903 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.63.061903'>10.1103/PhysRevE.63.061903</ext-link>

[209] Zolotaryuk A. V., Christiansen P. L., Savin A. V., “Two-dimensional dynamics of a free molecular chain with a secondary structure”, Physical Review E, 54 (1996), 3881–3894 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.54.3881'>10.1103/PhysRevE.54.3881</ext-link>

[210] Muto V., Lomdahl P. S., Christiansen P. L., “Two-dimensional discrete model for DNA dynamics: Longitudinal wave propagation and denaturation”, Physical Review A, 42 (1990), 7452–7458 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.42.7452'>10.1103/PhysRevA.42.7452</ext-link>

[211] Muto V., “Soliton Oscillations for DNA Dynamics”, Acta Applicandae Mathematicae, 15:1 (2011), 5–15 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/s10440-010-9564-8'>10.1007/s10440-010-9564-8</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2812973'>2812973</ext-link><ext-link ext-link-type='zbl-item-id' href='https://zbmath.org/?q=an:1221.92012'>1221.92012</ext-link>

[212] Alexandrov B. S., Wille L. T., Rasmussen K. O., Bishop A. R., Blagoev K. B., “Bubble statistics and dynamics in double-stranded DNA”, Physical review E, 74 (2006), 050901(R) <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.74.050901'>10.1103/PhysRevE.74.050901</ext-link>

[213] Altan-Bonnet G., Libchaber A., Krichevsky O., “Bubble Dynamics in Double-Stranded DNA”, Physical Review Letters, 90 (2003), 138101 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.90.138101'>10.1103/PhysRevLett.90.138101</ext-link>

[214] Sobell H. M., “Actinomycin and DNA transcription”, PNAS USA, 82 (1985), 5328–5331 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.82.16.5328'>10.1073/pnas.82.16.5328</ext-link>

[215] Cluzel P., Lebrun A., Heller C., Lavery R., Viovy J. L., Chatenay D., Caron F., “DNA: an extensible molecule”, Science, 271 (1996), 792–794 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.271.5250.792'>10.1126/science.271.5250.792</ext-link>

[216] Techera M., Daemen L. L., Prohofsky E. W., “Analysis of a nonlinear model for the DNA double helix: Energy transfer in an inhomogeneous chain”, Physical Review A, 42 (1990), 1008–1011 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevA.42.1008'>10.1103/PhysRevA.42.1008</ext-link>

[217] Muto V., “Local Denaturation in DNA Molecules”, Journal of Biological Physics, 19 (1993), 113–122 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/BF00700255'>10.1007/BF00700255</ext-link>

[218] Forinash K., Bishop A. R., Lomdahl P. S., “Nonlinear dynamics in a double-chain model of DNA”, Physical Review B, 43 (1991), 10743–10750 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevB.43.10743'>10.1103/PhysRevB.43.10743</ext-link>

[219] Forinash K., Peyrard M., Malomed B., “Interaction of discrete breathers with impurity modes”, Physical Review E, 49 (1994), 3400–3411 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.49.3400'>10.1103/PhysRevE.49.3400</ext-link>

[220] Chela-Fiores J., Migoni R. L., “CG Methylation in DNA Transcription”, International Journal of Theoretical Physics, 29 (1990), 853–862 <ext-link ext-link-type='doi' href='https://doi.org/10.1007/BF00675102'>10.1007/BF00675102</ext-link>

[221] Campa A., Giansanti A., “Experimental tests of the Peyrard–Bishop model applied to the melting of very short DNA chains”, Physical Review E, 58 (1998), 3585–3588 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.58.3585'>10.1103/PhysRevE.58.3585</ext-link>

[222] Lavery R., Lebrun A., Allemand J.-F., Bensimon D., Croquette V., “Structure and mechanics of single biomolecules: experiment and simulation”, Journal of Physics: Condensed Matter, 14 (2002), R383–R414 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/0953-8984/14/14/202'>10.1088/0953-8984/14/14/202</ext-link>

[223] Bustamante C., Smith S. B., Liphardt J., Smith D., “Single-molecule studies of DNA mechanics”, Current Opinion in Structural Biology, 10 (2000), 279–285 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0959-440X(00)00085-3'>10.1016/S0959-440X(00)00085-3</ext-link>

[224] Smith S. B., Finzi L., Bustamante C., “Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads”, Science, 258 (1992), 1122–1126 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.1439819'>10.1126/science.1439819</ext-link>

[225] Bustamante C., Marko J. F., Siggia E. D., Smith S., “Entropic elasticity of lambda-phage DNA”, Science, 265 (1994), 1599–600 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.8079175'>10.1126/science.8079175</ext-link>

[226] Smith S. B., Cui Y., Bustamante C., “Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules”, Science, 271 (1996), 795–799 <ext-link ext-link-type='doi' href='https://doi.org/10.1126/science.271.5250.795'>10.1126/science.271.5250.795</ext-link>

[227] Allemand J. F., Bensimon D., Lavery R., Croquette V., “Stretched and overwound DNA forms a Pauling-like structure with exposed bases”, PNAS USA, 95 (1998), 14152–14157 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.95.24.14152'>10.1073/pnas.95.24.14152</ext-link>

[228] Clausen-Schaumann H., Rief M., Tolksdorf C., Gaub H. E., “Mechanical Stability of Single DNA Molecules”, Biophysical Journal, 78 (2000), 1997–2007 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0006-3495(00)76747-6'>10.1016/S0006-3495(00)76747-6</ext-link>

[229] Rief M., Clausen-Schaumann H., Gaub H. E., “Sequence-dependent mechanics of single DNA molecules”, Nature Structural Biology, 6 (1999), 346–349 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/7582'>10.1038/7582</ext-link>

[230] Bockelmann U., Essevaz-Roulet B., Heslot F., “Molecular Stick-Slip Motion Revealed by Opening DNA with Piconewton Forces”, Physical Review Letters, 79 (1997), 4489–4492 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.79.4489'>10.1103/PhysRevLett.79.4489</ext-link>

[231] Essevaz-Ruolet B., Bockelmann U., Heslot F., “Mechanical separation of the complementary strands of DNA”, PNAS USA, 94 (1997), 11935–11940 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.94.22.11935'>10.1073/pnas.94.22.11935</ext-link>

[232] Bockelmann U., Thomen Ph., Essevaz-Roulet B., Viasnoff V., Heslot F., “Unzipping DNA with Optical Tweezers: High Sequence Sensitivity and Force Flips”, Biophysical Journal, 82 (2002), 1537–1553 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0006-3495(02)75506-9'>10.1016/S0006-3495(02)75506-9</ext-link>

[233] Bockelmann U., Viasnoff V., “Theoretical Study of Sequence-Dependent Nanopore Unzipping of DNA”, Biophysical Journal, 94 (2008), 2716–2724 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.107.111732'>10.1529/biophysj.107.111732</ext-link>

[234] Benham C. J., “Theoretical analysis of heteropolymeric transitions in superhelical DNA molecules of specified sequence”, The Journal of Chemical Physics, 92 (1990), 6294–6305 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.458353'>10.1063/1.458353</ext-link>

[235] Benham C. J., “Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci”, PNAS USA, 90 (1993), 2999–3003 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.90.7.2999'>10.1073/pnas.90.7.2999</ext-link>

[236] Benham C. J., “Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions”, Journal of Molecular Biology, 255 (1996), 425–434 <ext-link ext-link-type='doi' href='https://doi.org/10.1006/jmbi.1996.0035'>10.1006/jmbi.1996.0035</ext-link>

[237] Fye R. M., Benham C. J., “Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA”, Physical Review E, 59 (1999), 3408–3426 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.59.3408'>10.1103/PhysRevE.59.3408</ext-link>

[238] Rudnick J., Bruinsma R., “Effects of torsional strain on thermal denaturation of DNA”, Physical Review E, 65 (2002), 030902(R) <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.65.030902'>10.1103/PhysRevE.65.030902</ext-link>

[239] Hwa T., Marinari E., Sneppen K., Tang L. H., “Localization of denaturation bubbles in random DNA sequences”, PNAS USA, 100 (2003), 4411–4416 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.0736291100'>10.1073/pnas.0736291100</ext-link>

[240] Michoel T., Van de Peer Y., “Helicoidal transfer matrix model for inhomogeneous DNA melting”, Physical Review E, 73 (2006), 011908 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.73.011908'>10.1103/PhysRevE.73.011908</ext-link>

[241] Nelson P., “Transport of torsional stress in DNA”, PNAS USA, 96 (1999), 14342–14347 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.96.25.14342'>10.1073/pnas.96.25.14342</ext-link>

[242] Benham C. J., Singh R. R. P., Comment on “Can One Predict DNA Transcription Start Sites by Studying Bubbles?”, Physical Review Letters, 97 (2006), 059801 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.97.059801'>10.1103/PhysRevLett.97.059801</ext-link>

[243] Benham C., Kohwi-Shigematsu T., Bode J., “Stress-induced Duplex DNA Destabilization in Scaffold/Matrix Attachment Regions”, Journal of Molecular Biology, 274 (1997), 181–196 <ext-link ext-link-type='doi' href='https://doi.org/10.1006/jmbi.1997.1385'>10.1006/jmbi.1997.1385</ext-link>

[244] Wang H., Benham C. J., “Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress”, BMC Bioinformatics, 7 (2006), 248 <ext-link ext-link-type='doi' href='https://doi.org/10.1186/1471-2105-7-248'>10.1186/1471-2105-7-248</ext-link>

[245] Trovato F., Tozzini V., “Supercoiling and Local Denaturation of Plasmids with a Minimalist DNA Model”, Journal of Physical Chemistry B, 112 (2008), 13197–13200 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/jp807085d'>10.1021/jp807085d</ext-link>

[246] Kumar S., Li M. S., “Biomolecules under mechanical force”, Physics Reports, 486 (2010), 1–74 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.physrep.2009.11.001'>10.1016/j.physrep.2009.11.001</ext-link>

[247] Marenduzzo D., Bhattacharjee S. M., Maritan A., Orlandini E., Seno F., “Dynamical Scaling of the DNA Unzipping Transition”, Physical Review Letters, 88 (2002), 028102 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.88.028102'>10.1103/PhysRevLett.88.028102</ext-link>

[248] Kapri R., Bhattacharjee S. M., Seno F., “Complete Phase Diagram of DNA Unzipping: Eye, Y-Fork, and Triple Point”, Physical Review Letters, 93 (2004), 248102 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.93.248102'>10.1103/PhysRevLett.93.248102</ext-link>

[249] Kumar S., Giri D., Bhattacahrjee S. M., “Force induced triple point for interacting polymers”, Physical Review E, 71 (2005), 051804 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.71.051804'>10.1103/PhysRevE.71.051804</ext-link>

[250] Giri D., Kumar S., “Effects of the eye phase in DNA unzipping”, Physical Review E, 73 (2006), 050903(R) <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.73.050903'>10.1103/PhysRevE.73.050903</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2336754'>2336754</ext-link>

[251] Kumar S., Giri D., “Probability distribution analysis of force induced unzipping of DNA”, The Journal of Chemical Physics, 125 (2006), 044905 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.2219115'>10.1063/1.2219115</ext-link>

[252] Singh A. R., Giri D., Kumar S., “Force induced melting of the constrained DNA”, The Journal of Chemical Physics, 32 (2010), 235105 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.3427587'>10.1063/1.3427587</ext-link>

[253] Lubensky D. K., Nelson D. R., “Pulling Pinned Polymers and Unzipping DNA”, Physical Review Letters, 85 (2000), 1572–1575 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.85.1572'>10.1103/PhysRevLett.85.1572</ext-link>

[254] Lubensky D. K., Nelson D. R., “Single molecule statistics and the polynucleotide unzipping transition”, Physical Review E, 65 (2002), 031917 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.65.031917'>10.1103/PhysRevE.65.031917</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1934928'>1934928</ext-link>

[255] Thompson R. E., Siggia E. D., “Physical limits on the mechanical measurement of the secondary structure of biomolecules”, Europhysics Letters, 31 (1995), 335–340 <ext-link ext-link-type='doi' href='https://doi.org/10.1209/0295-5075/31/5-6/015'>10.1209/0295-5075/31/5-6/015</ext-link>

[256] Viovy J. L., Heller C., Caron F., Cluzel P., Chatenay D., “Sequencing of DNA by mechanical opening of the double helix: a theoretical evaluation”, Comptes rendus de l' Academie des sciences Paris (Life Sciences), 317 (1994), 795–800

[257] Peyrard M., Using DNA to probe nonlinear localized excitations?, Europhysics Letters, 44 (1998), 271–277 <ext-link ext-link-type='doi' href='https://doi.org/10.1209/epl/i1998-00469-9'>10.1209/epl/i1998-00469-9</ext-link>

[258] Krautbauer R., Rief M., Gaub H. E., “Unzipping DNA Oligomers”, Nano Letters, 3 (2003), 493–496 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/nl034049p'>10.1021/nl034049p</ext-link>

[259] Singh N., Singh Y., “Statistical theory of force-induced unzipping of DNA”, European Physical Journal E, 17 (2005), 7–19 <ext-link ext-link-type='doi' href='https://doi.org/10.1140/epje/i2004-10100-7'>10.1140/epje/i2004-10100-7</ext-link>

[260] Voulgarakis N. K., Redondo A., Bishop A. R., Rasmussen K. O., “Probing the Mechanical Unzipping of DNA”, Physical Review Letters, 96 (2006), 248101 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.96.248101'>10.1103/PhysRevLett.96.248101</ext-link>

[261] Zeng Y., Montrichok A., Zocchi G., “Bubble nucleation and cooperativity in DNA melting”, Journal of Molecular Biology, 339 (2004), 67–75 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/j.jmb.2004.02.072'>10.1016/j.jmb.2004.02.072</ext-link>

[262] Ares S., Voulgarakis N. K., Rasmussen K. O., Bishop A. R., “Bubble Nucleation and Cooperativity in DNA Melting”, Physical Review Letters, 94 (2005), 035504 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.94.035504'>10.1103/PhysRevLett.94.035504</ext-link>

[263] Metropolis N., Rosenbluth A. W., Rosenbluth M. N., Teller A. H., Teller E., “Equation of State Calculations by Fast Computing Machines”, The Journal of Chemical Physics, 21 (1953), 1087–1092 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1699114'>10.1063/1.1699114</ext-link>

[264] van Erp T. S., Cuesta-Lopez S., Peyrard M., “Bubbles and denaturation in DNA”, European Physical Journal E, 20 (2006), 421–434 <ext-link ext-link-type='doi' href='https://doi.org/10.1140/epje/i2006-10032-2'>10.1140/epje/i2006-10032-2</ext-link>

[265] van Erp T. S., Cuesta-Lopez S., Hagmann J.-G., Peyrard M., Can One Predict DNA Transcription Start Sites by Studying Bubbles?, Physical Review Letters, 95 (2005), 218104 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.95.218104'>10.1103/PhysRevLett.95.218104</ext-link>

[266] Wiegand R. C., Godson G. N., Radding C. N., “Specificity of the $S_1$ Nuclease from Aspergillus oryzae”, The Journal of Biological Chemistry, 250 (1975), 8848–8855

[267] Rapti Z., Smerzi A., Rasmussen K. O., Bishop A. R., Choi C. H., Usheva A., “Lengthscales and cooperativity in DNA bubble formation”, Europhysics Letters, 74 (2006), 540–546 <ext-link ext-link-type='doi' href='https://doi.org/10.1209/epl/i2005-10543-x'>10.1209/epl/i2005-10543-x</ext-link>

[268] Rapti Z., Smerzi A., Rasmussen K. O., Bishop A. R., “Healing length and bubble formation in DNA”, Physical Review E, 73 (2006), 051902 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.73.051902'>10.1103/PhysRevE.73.051902</ext-link>

[269] Choi C. H., Rapti Z., Gelev V., Hacker M. R., Alexandrov B., Park E. J., Park J. S., Horikoshi N., Smerzi A., Rasmussen K. O., Bishop A. R., Usheva A., “Profiling the Thermodynamic Softness of Adenoviral Promoters”, Biophysical Journal, 95 (2008), 597–608 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.107.123471'>10.1529/biophysj.107.123471</ext-link>

[270] Liu F., Tostesen E., Sundet J. K., Jenssen T.-K., Bock C., Jerstad G. I., Thilly W. G., Hovig E., “The Human Genomic Melting Map”, PLoS Computational Biology, 3:5 (2007), 0874–0886 <ext-link ext-link-type='doi' href='https://doi.org/10.1371/journal.pcbi.0030093'>10.1371/journal.pcbi.0030093</ext-link>

[271] Abeel T., Saeys Y., Bonnet E., Rouze P., Van de Peer Y., “Generic eukaryotic core promoter prediction using structural features of DNA”, Genome Research, 18 (2008), 310–323 <ext-link ext-link-type='doi' href='https://doi.org/10.1101/gr.6991408'>10.1101/gr.6991408</ext-link>

[272] Kantorovitz M. R., Rapti Z., Gelev V., Usheva A., “Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites”, BMC Bioinformatics, 11 (2010), 604 <ext-link ext-link-type='doi' href='https://doi.org/10.1186/1471-2105-11-604'>10.1186/1471-2105-11-604</ext-link>

[273] Alexandrov B. S., Gelev V., Yoo S. W., Bishop A. R., Rasmussen K. O., Usheva A., “Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter”, PLoS Computational Biology, 5 (2009), 1–10 <ext-link ext-link-type='doi' href='https://doi.org/10.1371/journal.pcbi.1000313'>10.1371/journal.pcbi.1000313</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=2501367'>2501367</ext-link>

[274] Alexandrov B. S., Gelev V., Monisova Y., Alexandrov L. B., Bishop A. R., Rasmussen K. O., Usheva A., “A nonlinear dynamic model of DNA with a sequence-dependent stacking term”, Nucleic Acids Research, 37 (2009), 2405–2410 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkp016'>10.1093/nar/gkp016</ext-link>

[275] Alexandrov B. S., Gelev V., Yoo S. W., Alexandrov L. B., Fukuyo Y., Bishop A. R., Rasmussen K. O., Usheva A., “DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation”, Nucleic Acids Research, 38 (2010), 1790–1795 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkp1084'>10.1093/nar/gkp1084</ext-link>

[276] Alexandrov B. S., Valtchinov V. I., Alexandrov L. B., Gelev V., Dagon Y., Bock J., Kohane I. S., Rasmussen K. O., Bishop A. R., Usheva A., “DNA Dynamics Is Likely to Be a Factor in the Genomic Nucleotide Repeats Expansions Related to Diseases”, PLoS One, 6 (2011), 1–6 <ext-link ext-link-type='doi' href='https://doi.org/10.1371/annotation/f68e9b71-cae1-4f9c-9308-a444d3ea753d'>10.1371/annotation/f68e9b71-cae1-4f9c-9308-a444d3ea753d</ext-link>

[277] Dornberger U., Leijon M., Fritzsche H., “High Base Pair Opening Rates in Tracts of GC Base Pairs”, The Journal of Biological Chemistry, 274 (1999), 6957–6962 <ext-link ext-link-type='doi' href='https://doi.org/10.1074/jbc.274.11.6957'>10.1074/jbc.274.11.6957</ext-link>

[278] Maiti S., Haupts U., Webb W. W., “Fluorescence correlation spectroscopy: Diagnostics for sparse molecules”, PNAS USA, 94 (1997), 11753–11757 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.94.22.11753'>10.1073/pnas.94.22.11753</ext-link>

[279] Bonnet G., Krichevsky O., Libchaber A., “Kinetics of conformational fluctuations in DNA hairpin-loops”, PNAS USA, 95 (1998), 8602–8606 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.95.15.8602'>10.1073/pnas.95.15.8602</ext-link>

[280] Krueger A., Protozanova E., Frank-Kamenetskii M. D., “Sequence-dependent base pair opening in DNA double helix”, Biophysical Journal, 90 (2006), 3091–3099 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.105.078774'>10.1529/biophysj.105.078774</ext-link>

[281] Gueron M., Kochoyan M., Leroy J. L., “A single mode of DNA base-pair opening drives imino proton exchange”, Nature, 328 (1987), 89–92 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/328089a0'>10.1038/328089a0</ext-link>

[282] Kochoyan M., Leroy J. L., Gueron M., “Proton Exchange and Base-pair Lifetimes in a Deoxy-duplex Containing a Purine-Pyrimidine Step and in the Duplex of Inverse Sequence”, Journal of Molecular Biology, 196 (1987), 599–609 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(87)90036-2'>10.1016/0022-2836(87)90036-2</ext-link>

[283] Leroy J. L., Kochoyan M., Huynh-Dinh T., Gueron M., “Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton”, Journal of Molecular Biology, 200 (1988), 223–238 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(88)90236-7'>10.1016/0022-2836(88)90236-7</ext-link>

[284] Kochoyan M., Lancelot G., Leroy J. L., “Study of structure, base-pair opening kinetics and proton exchange mechanism of the d(AATTGCAATT) self-complementary oligodeoxynucleotide in solution”, Nucleic Acids Research, 16 (1988), 7685–7702 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/16.15.7685'>10.1093/nar/16.15.7685</ext-link>

[285] Moe J. G., Russu I. M., “Proton exchange and base-pair opening kinetics in 5'-d(CGCGAATTCGCG)-3' and related dodecamers”, Nucleic Acids Research, 18 (1990), 821–827 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/18.4.821'>10.1093/nar/18.4.821</ext-link>

[286] Leroy J. L., Gao X. L., Gueron M., Patel D. J., “Proton exchange and internal motions in two chromomycin dimer-DNA oligomer complexes”, Biochemistry, 30 (1991), 5653–5661 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00237a003'>10.1021/bi00237a003</ext-link>

[287] David S. S., Williams S. D., “Chemistry of glycosylases and endonucleases involved in base-excision repair”, Chemical Reviews, 98 (1998), 1221–1262 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/cr980321h'>10.1021/cr980321h</ext-link>

[288] Stivers J. T., “Site-Specific DNA Damage Recognition by Enzyme-Induced Base Flipping”, Progress in Nucleic Acid Research and Molecular Biology, 77 (2004), 37–65 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0079-6603(04)77002-6'>10.1016/S0079-6603(04)77002-6</ext-link>

[289] Klimasauskas S., Kumar S., Roberts R. J., Cheng X., “HhaI methyltransferase flips its target base out of the DNA helix”, Cell, 76 (1994), 57–69 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0092-8674(94)90342-5'>10.1016/0092-8674(94)90342-5</ext-link>

[290] Reinisch K. M., Chen L., Verdine G. L., Lipscomb W. N., “The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing”, Cell, 82 (1995), 143–153 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0092-8674(95)90060-8'>10.1016/0092-8674(95)90060-8</ext-link>

[291] Cheng X., Roberts R. J., “AdoMet-dependent methylation, DNA methyltransferases and base flipping”, Nucleic Acids Research, 29 (2001), 3784–3795 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/29.18.3784'>10.1093/nar/29.18.3784</ext-link>

[292] Lau A. Y., Wyatt M. D., Glassner B. J., Samson L. D., Ellenberger T., “Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG”, PNAS USA, 97 (2000), 13573–13578 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.97.25.13573'>10.1073/pnas.97.25.13573</ext-link>

[293] Hollis T., Ichikawa Y., Ellenberger T., “DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase,Escherichia coli AlkA”, EMBO Journal, 19 (2000), 758–766 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/emboj/19.4.758'>10.1093/emboj/19.4.758</ext-link>

[294] Fromme J. C., Verdine G. L., “DNA Lesion Recognition by the Bacterial Repair Enzyme MutM”, The Journal of Biological Chemistry, 278 (2003), 51543–51548 <ext-link ext-link-type='doi' href='https://doi.org/10.1074/jbc.M307768200'>10.1074/jbc.M307768200</ext-link>

[295] Lyakhov I. G., Hengen P. N., Rubens D., Schneider T. D., “The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping”, Nucleic Acids Research, 29 (2001), 4892–4900 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/29.23.4892'>10.1093/nar/29.23.4892</ext-link>

[296] Schneider T. D., “Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation”, Nucleic Acids Research, 29 (2001), 4881–4891 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/29.23.4881'>10.1093/nar/29.23.4881</ext-link>

[297] Gueron M., Leroy J. L., “Studies of base pair kinetics by NMR measurement of proton exchange”, Methods in Enzymology, 261 (1995), 383–413 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0076-6879(95)61018-9'>10.1016/S0076-6879(95)61018-9</ext-link>

[298] Crothers D. M., Cole P. E., Hilbers C. W., Shulman R. G., “The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA”, Journal of Molecular Biology, 87 (1974), 63–72 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(74)90560-9'>10.1016/0022-2836(74)90560-9</ext-link>

[299] Warmlander S., Sen A., Leijon M., “Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: evidence for a secondary long-lived open state of the base pair”, Biochemistry, 39 (2000), 607–615 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi991863b'>10.1021/bi991863b</ext-link>

[300] Folta-Stogniew E., Russu I. M., “Base-catalysis of imino proton exchange in DNA: effects of catalyst upon DNA structure and dynamics”, Biochemistry, 35 (1996), 8439–8449 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi952932z'>10.1021/bi952932z</ext-link>

[301] Leijon M., Leroy J. L., “Internal motions of nucleic acid structures and the determination of base-pair lifetimes”, Biochimie, 79 (1997), 775–779 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0300-9084(97)86936-2'>10.1016/S0300-9084(97)86936-2</ext-link>

[302] Forsen S., Hoffman R. A., “Study of Moderately Rapid Chemical Exchange Reactions by Means of Nuclear Magnetic Double Resonance”, The Journal of Chemical Physics, 39 (1963), 2892–2901 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.1734121'>10.1063/1.1734121</ext-link>

[303] Mihailescu M. R., Russu I. M., “A signature of the T$\to$R transition in human hemoglobin”, PNAS USA, 98 (2001), 3773–3777 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.071493598'>10.1073/pnas.071493598</ext-link>

[304] Snoussi K., Leroy J. L., “Imino proton exchange and base-pair kinetics in RNA duplexes”, Biochemistry, 31 (2001), 8898–8904 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi010385d'>10.1021/bi010385d</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1946416'>1946416</ext-link>

[305] Snoussi K., Leroy J. L., “Alteration of A.T base-pair opening kinetics by the ammonium cation in DNA A-tracts”, Biochemistry, 41 (2002), 12467–12474 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi020184p'>10.1021/bi020184p</ext-link>

[306] Varnai P., Canalia M., Leroy J. L., “Opening mechanism of G.T/U pairs in DNA and RNA duplexes: a combined study of imino proton exchange and molecular dynamics simulation”, Journal of American Chemical Society, 126 (2004), 14659–14667 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/ja0470721'>10.1021/ja0470721</ext-link>

[307] Chen C., Russu I. M., “Sequence-dependence of the energetics of opening of at basepairs in DNA”, Biophysical Journal, 87 (2004), 2545–2551 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.104.045179'>10.1529/biophysj.104.045179</ext-link>

[308] Englander S. W., “A Hydrogen Exchange Method Using Tritium and Sephadex: Its Application to Ribonuclease”, Biochemistry, 2 (1963), 798–807 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00904a030'>10.1021/bi00904a030</ext-link>

[309] Printz M. P., von Hippel P. H., “Hydrogen Exchange Studies of DNA Structure”, PNAS USA, 53 (1965), 363–370 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.53.2.363'>10.1073/pnas.53.2.363</ext-link>

[310] Williams M. N., Crothers D. M., “Binding kinetics of mercury(II) to polyribonucleotides”, Biochemistry, 14 (1975), 1944–1951 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00680a022'>10.1021/bi00680a022</ext-link>

[311] Wilcoxon J., Schurr J. M., “Temperature dependence of the dynamic light scattering of linear phi29 DNA: Implications for spontaneous opening of the double helix”, Biopolymers, 22 (1983), 2273–2321 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.360221011'>10.1002/bip.360221011</ext-link>

[312] Frank-Kamenetskii M. D., “Fluctuationsal Motility of DNA”, Structure and Motion: Membranes, Nucleic Acids and Proteins, eds. Clemeti E., Corongiu G., Sarma M. H., Sarma R. H., Adenine Press, Guilderland, 1985, 417–422

[313] Leroy J.-L., Broseta D., Gueron M., “Proton exchange and base-pair kinetics of poly(rA):poly(rU) and poly(rI):poly(rC)”, Journal of Molecular Biology, 184, 165–178 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(85)90050-6'>10.1016/0022-2836(85)90050-6</ext-link>

[314] Leroy J. L., Bolo N., Figueroa N., Plateau P., Gueron M., “Internal motions of transfer RNA: a study of exchanging protons by magnetic resonance”, Journal of Biomolecular Structure and Dynamics, 2 (1985), 915–939 <ext-link ext-link-type='doi' href='https://doi.org/10.1080/07391102.1985.10507609'>10.1080/07391102.1985.10507609</ext-link>

[315] Kochoyan M., Leroy J. L., Gueron M., “Processes of base-pair opening and proton exchange in Z-DNA”, Biochemistry, 29 (1990), 4799–4805 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00472a008'>10.1021/bi00472a008</ext-link>

[316] Leijon M., Graslund A., “Effects of sequence and length on imino proton exchange and base pair opening kinetics in DNA oligonucleotide duplexes”, Nucleic Acids Research, 20 (1992), 5339–5343 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/20.20.5339'>10.1093/nar/20.20.5339</ext-link>

[317] Nonin S., Leroy J. L., Gueron M., “Terminal base pairs of oligodeoxynucleotides: imino proton exchange and fraying”, Biochemistry, 34 (1995), 10652–10659 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00033a041'>10.1021/bi00033a041</ext-link>

[318] Moe J. G., Russu I. M., “Kinetics and energetics of base-pair opening in 5'-d(CGCGAATTCGCG)-3' and a subsituted dodecamer containing G.T mismatches”, Biochemistry, 31 (1992), 8421–8428 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00151a005'>10.1021/bi00151a005</ext-link>

[319] Coman D., Russu I. M., “Base pair opening in three DNA-unwinding elements”, Journal of Biological Chemistry, 280 (2005), 20216–20221 <ext-link ext-link-type='doi' href='https://doi.org/10.1074/jbc.M502773200'>10.1074/jbc.M502773200</ext-link>

[320] Leroy J. L., Charretier E., Kochoyan M., Gueron M., “Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature”, Biochemistry, 27 (1988), 8894–8898 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00425a004'>10.1021/bi00425a004</ext-link>

[321] Yoon C., Prive G. G., Goodsell D. S., Dickerson R. E., “Structure of an alternating-B DNA helix and its relationship to A-tract DNA”, PNAS USA, 85 (1988), 6332–6336 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.85.17.6332'>10.1073/pnas.85.17.6332</ext-link>

[322] Edwards K. J., Brown D. G., Spink N., Skelly J. V., Neidle S., “Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)$_2$. An examination of propeller twist and minor-groove water structure at 2.2 Åresolution”, Journal of Moleclar Biology, 226 (1992), 1161–1173 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/0022-2836(92)91059-X'>10.1016/0022-2836(92)91059-X</ext-link>

[323] Shatzky-Schwartz M., Arbuckle N. D., Eisenstein M., Rabinovich D., Bareket-Samish A., Haran T. E., Luisi B. F., Shakked Z., “X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature”, Journal of Molecular Biology, 267 (1997), 595–623 <ext-link ext-link-type='doi' href='https://doi.org/10.1006/jmbi.1996.0878'>10.1006/jmbi.1996.0878</ext-link>

[324] Leijon M., Zdunek J., Fritzsche H., Sklenar H., Graslund A., “NMR studies and restrained-molecular-dynamics calculations of a long A+T-rich stretch in DNA. Effects of phosphate charge and solvent approximations”, European Journal of Biochemistry, 234 (1995), 832–842 <ext-link ext-link-type='doi' href='https://doi.org/10.1111/j.1432-1033.1995.832_a.x'>10.1111/j.1432-1033.1995.832_a.x</ext-link>

[325] Warmlander S., Sponer J. E., Sponer J., Leijon M., “The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA”, Journal of Biological Chemistry, 277 (2002), 28491–28497 <ext-link ext-link-type='doi' href='https://doi.org/10.1074/jbc.M202989200'>10.1074/jbc.M202989200</ext-link>

[326] Movileanu L., Benevides J. M., Thomas G. J. Jr., “Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA”, Nucleic Acids Research, 30 (2002), 3767–3777 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkf471'>10.1093/nar/gkf471</ext-link>

[327] Dornberger U., Spackova N., Walter A., Gollmick F. A., Sponer J., Fritzsche H., “Solution structure of the dodecamer d-(CATGGGCC-CATG)2 is B-DNA. Experimental and molecular dynamics study”, Journal of Biomolecular Structure & Dynamics, 19 (2001), 159–174 <ext-link ext-link-type='doi' href='https://doi.org/10.1080/07391102.2001.10506728'>10.1080/07391102.2001.10506728</ext-link>

[328] Denisov E. T., Kinetika gomogennykh khimicheskikh reaktsii, Vysshaya shkola, M., 1978, 139 pp.

[329] Leijon M., Sehlstedt U., Nielsen P. E., Graslund A., “Unique base-pair breathing dynamics in PNA-DNA hybrids”, Journal of Molecular Biology, 271 (1997), 438–455 <ext-link ext-link-type='doi' href='https://doi.org/10.1006/jmbi.1997.1153'>10.1006/jmbi.1997.1153</ext-link>

[330] Moe J. G., Folta-Stogniew E., Russu I. M., “Energetics of base pair opening in a DNA dodecamer containing an $\mathrm{A_3T_3}$ tract”, Nucleic Acids Research, 23 (1995), 1984–1989 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/23.11.1984'>10.1093/nar/23.11.1984</ext-link>

[331] Coman D., Russu I. M., “A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA”, Biophysical Journal, 89 (2005), 3285–3292 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.105.065763'>10.1529/biophysj.105.065763</ext-link>

[332] Goddard N. L., Bonnet G., Krichevsky O., Libchaber A., “Sequence Dependent Rigidity of Single Stranded DNA”, Physical Review Letters, 85 (2000), 2400–2403 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevLett.85.2400'>10.1103/PhysRevLett.85.2400</ext-link>

[333] Movileanu L., Benevides J. M., Thomas G. I. Jr., “Temperature Dependence of the Raman Spectrum of DNA. II: Raman Signatures of Premelting and Melting Transitions of Poly(dA)-Poly(dT) and Comparison with Poly(dA-dT)-Poly(dA-dT)”, Biopolymers, 63 (2002), 181–194 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.10022'>10.1002/bip.10022</ext-link>

[334] Peyrard M., Cuesta-Lopez S., Angelov D., “Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules”, Journal of Physics: Condensed Matter, 21:3 (2009), 034103 <ext-link ext-link-type='doi' href='https://doi.org/10.1088/0953-8984/21/3/034103'>10.1088/0953-8984/21/3/034103</ext-link>

[335] Freier S. M., Hill K. O., Dewey T. G., Marky L. A., Breslauer K. J., Turner D. H., “Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid)”, Biochemistry, 20 (1981), 1419–1426 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi00509a003'>10.1021/bi00509a003</ext-link>

[336] Gueron M., Shulman R. G., Eisinger J., “Energy transfer in dinucleotides”, PNAS USA, 56 (1966), 814–818 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.56.3.814'>10.1073/pnas.56.3.814</ext-link>

[337] Warshaw M. M., Tinoco I. Jr., “Absorption and optical rotatory dispersion of six dinucleoside phosphates”, Journal of Molecular Biology, 13 (1965), 54–64 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2836(65)80079-1'>10.1016/S0022-2836(65)80079-1</ext-link>

[338] Leng M., Felsenfeld G., “A study of polyadenylic acid at neutral pH”, Journal of Molecular Biology, 15 (1966), 455–466 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2836(66)80121-3'>10.1016/S0022-2836(66)80121-3</ext-link>

[339] Brahms J., Michelson A. M., Van Holde K. E., “Adenylate Olygomers in Single- and Double-strand Conformation”, Journal of Molecular Biology, 15 (1966), 467–488 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2836(66)80122-5'>10.1016/S0022-2836(66)80122-5</ext-link>

[340] Adler A., Grossman L., Fasman G. D., “Single-stranded oligomers and polymers of cytidylic and 2'-deoxycytidylic acids: comparative optical rotatory studies”, PNAS USA, 57 (1967), 423–430 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.57.2.423'>10.1073/pnas.57.2.423</ext-link>

[341] Vesnaver G., Breslauer K. J., “The contribution of DNA single-stranded order to the thermodynamics of duplex formation”, PNAS USA, 88 (1991), 3569–3573 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.88.9.3569'>10.1073/pnas.88.9.3569</ext-link>

[342] Holbrook J. A., Capp M. W., Saecker R. M., Record M. T. Jr., “Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices”, Biochemistry, 38 (1999), 8409–8422 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/bi990043w'>10.1021/bi990043w</ext-link>

[343] Zhou J., Gregurick S. K., Krueger S., Schwarz F. P., “Conformational Changes in Single-Strand DNA as a Function of Temperature by SANS”, Biophysical Journal, 90 (2006), 544–551 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.105.071290'>10.1529/biophysj.105.071290</ext-link>

[344] Mills J. B., Vacano E., Hagerman P. J., “Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of Poly(dT) and Poly(dA)”, Journal of Molecular Biology, 285 (1999), 245–257 <ext-link ext-link-type='doi' href='https://doi.org/10.1006/jmbi.1998.2287'>10.1006/jmbi.1998.2287</ext-link>

[345] Benight A. S., Wartell R. M., Howell D. K., “Theory agrees with experimental thermal denaturation of short DNA restriction fragments”, Nature, 289 (1981), 203–205 <ext-link ext-link-type='doi' href='https://doi.org/10.1038/289203a0'>10.1038/289203a0</ext-link>

[346] Tibanyenda N., De Bruin S. H., Haasnoot C. A., van der Marel G. A., van Boom J. H., Hilbers C. W., “The effect of single base-pair mismatches on the duplex stability of d(T-A-T-T-A-A-T-A-T-C-A-A-G-T-T-G):d(C-A-A-C-T-T-G-A-T-A-T-T-A-A-T-A)”, European Journal of Biochemistry, 139 (1984), 19–27 <ext-link ext-link-type='doi' href='https://doi.org/10.1111/j.1432-1033.1984.tb07970.x'>10.1111/j.1432-1033.1984.tb07970.x</ext-link>

[347] Cuesta-Lopez S., Menoni H., Angelov D., Peyrard M., “Guanine radical chemistry reveals the effect of thermal fluctuations in gene promoter regions”, Nucleic Acids Research, 39 (2011), 5276–5283 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/gkr096'>10.1093/nar/gkr096</ext-link>

[348] Coll M., Frederick C. A., Wang A. H., Rich A., “A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG)$_2$ and its complex with distamycin”, PNAS USA, 84 (1987), 8385–8389 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.84.23.8385'>10.1073/pnas.84.23.8385</ext-link>

[349] Ting J. J.-L., Peyrard M., “Effective breather trapping mechanism for DNA transcription”, Physical Review E, 53 (1996), 1011–1020 <ext-link ext-link-type='doi' href='https://doi.org/10.1103/PhysRevE.53.1011'>10.1103/PhysRevE.53.1011</ext-link><ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1412088'>1412088</ext-link>

[350] Ares S., Kalosakas G., “Distribution of Bubble Lengths in DNA”, Nano Letters, 7 (2007), 307–311 <ext-link ext-link-type='doi' href='https://doi.org/10.1021/nl062304a'>10.1021/nl062304a</ext-link>

[351] Krichevskii O. M., Lichnoe soobschenie, 6.11.2012

[352] Padro J. A., Saiz L., Guardia E., “Hydrogen bonding in liquid alcohols: a computer simulation study”, Journal of Molecular Structure, 416 (1997), 243–248 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0022-2860(97)00038-0'>10.1016/S0022-2860(97)00038-0</ext-link>

[353] Guardia E., Marti J., Padro J. A., Saiz L., Komolkin A. V., “Dynamics in hydrogen bonded liquids: water and alcohols”, Journal of Molecular Liquids, 96–97 (2002), 3–17 <ext-link ext-link-type='doi' href='https://doi.org/10.1016/S0167-7322(01)00342-7'>10.1016/S0167-7322(01)00342-7</ext-link>

[354] Breslauer K. J., Frank R., Blocker H., Marky L. A., “Predicting DNA duplex stability from the base sequence”, PNAS USA, 83 (1986), 3746–3750 <ext-link ext-link-type='doi' href='https://doi.org/10.1073/pnas.83.11.3746'>10.1073/pnas.83.11.3746</ext-link>

[355] Nonin S., Leroy J. L., Gueron M., “Acid-induced exchange of the imino proton in G.C pairs”, Nucleic Acids Research, 24 (1996), 586–595 <ext-link ext-link-type='doi' href='https://doi.org/10.1093/nar/24.4.586'>10.1093/nar/24.4.586</ext-link>

[356] Nakahara M., Wakai C., “Inertial and attractive potential effects on rotation of solitary water molecules in apolar and polar solvents”, The Journal of Chemical Physics, 97 (1992), 4413 <ext-link ext-link-type='doi' href='https://doi.org/10.1063/1.463910'>10.1063/1.463910</ext-link>

[357] Every A. E., Russu I. M., “Probing the Role of Hydrogen Bonds in the Stability of Base Pairs in Double-Helical DNA”, Biopolymers, 87 (2007), 165–173 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.20811'>10.1002/bip.20811</ext-link>

[358] Fixman M., Friere J., “Theory of DNA melting curves”, Biopolymers, 16 (1977), 2693–2704 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.1977.360161209'>10.1002/bip.1977.360161209</ext-link>

[359] Poland D., “Recursion Relation Generation of Probability Profiles for Specific-Sequence Macromolecules with Long-Range Correlations”, Biopolymers, 13 (1974), 1859–1871 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.1974.360130916'>10.1002/bip.1974.360130916</ext-link>

[360] Gotoh O., Tagashira Y., “Stabilities of Nearest-Neighbor Doublets in Double-Helical DNA Determined by Fitting Calculated Melting Profiles to Observed Profiles”, Biopolymers, 20 (1981), 1033–1042 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.1981.360200513'>10.1002/bip.1981.360200513</ext-link>

[361] Gordan R., Hartemink A. J., “Using DNA duplex stability information for transcription factor binding site discovery”, Pacfic Symposium on Biocomputing, 13 (2008), 453–464

[362] Klump H., Ackermann T., “Experimental thermodynamics of the helix-random coil transition. IV: Influence of the base composition of DNA on the transition enthalpy”, Biopolymers, 10 (1971), 513–522 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.360100307'>10.1002/bip.360100307</ext-link>

[363] Marky L. A., Breslauer K. J., “Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules”, Biopolymers, 21 (1982), 2185–2194 <ext-link ext-link-type='doi' href='https://doi.org/10.1002/bip.360211107'>10.1002/bip.360211107</ext-link>

[364] Chaplin M., Water Clusters: Overview, (data obrascheniya: 21.10.2013) <ext-link ext-link-type='uri' href='http://www.lsbu.ac.uk/water/abstrct.html'>http://www.lsbu.ac.uk/water/abstrct.html</ext-link>

[365] Klyachko N. L., “Fermenty — biologicheskie katalizatory: osnovnye printsipy deistviya”, Sorosovskii obrazovatelnyi zhurnal, 1997, no. 3, 58–63 <ext-link ext-link-type='mr-item-id' href='http://mathscinet.ams.org/mathscinet-getitem?mr=1446101'>1446101</ext-link>

[366] Banerjee A., Sobell H. M., “Presence of nonlinear excitations in DNA structure and their relationship to DNA premelting and to drug intercalation”, Journal of Biomolecular Structure and Dynamics, 1 (1983), 253–262 <ext-link ext-link-type='doi' href='https://doi.org/10.1080/07391102.1983.10507438'>10.1080/07391102.1983.10507438</ext-link>

[367] de los Santos F., Al Hammal O., Munoz M. A., “Simplified Langevin approach to the Peyrard–Bishop–Dauxois model of DNA”, Physical Review E, 77 (2008), 032901

[368] Beveridge D. L., Barreiro G., Byun K. S., Case D. A., Cheatham T. E. 3rd, Dixit S. B., Giudice E., Lankas F., Lavery R., Maddocks J. H., Osman R., Seibert E., Sklenar H., Stoll G., Thayer K. M., Varnai P., Young M. A., “Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I: Research Design and Results on d(CpG) Steps”, Biophysical Journal, 87 (2004), 3799–3813 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.104.045252'>10.1529/biophysj.104.045252</ext-link>

[369] Dixit S. B., Beveridge D. L., Case D. A., Cheatham T. E. 3rd, Giudice E., Lankas F., Lavery R., Maddocks J. H., Osman R., Sklenar H., Thayer K. M., Varnai P., “Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps”, Biophysical Journal, 89 (2005), 3721–3740 <ext-link ext-link-type='doi' href='https://doi.org/10.1529/biophysj.105.067397'>10.1529/biophysj.105.067397</ext-link>