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Journal articles on the topic 'DNA thermodynamics'

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Published: 10 December 2022
Last updated: 28 January 2023

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1

SARAI, Akinori. "Thermodynamics of DNA-protein." Seibutsu Butsuri 35, no. 1 (1995): 20–24. http://dx.doi.org/10.2142/biophys.35.20.

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2

Lu, Min, Qiu Guo, Luis A. Marky, Nadrian C. Seeman, and Neville R. Kallenbach. "Thermodynamics of DNA branching." Journal of Molecular Biology 223, no. 3 (February 1992): 781–89. http://dx.doi.org/10.1016/0022-2836(92)90989-w.

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3

Rozikov, U. A. "Thermodynamics of DNA–RNA renaturation." International Journal of Geometric Methods in Modern Physics 18, no. 06 (March 5, 2021): 2150096. http://dx.doi.org/10.1142/s0219887821500961.

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We consider a new model which consists of a DNA together with a RNA. Here, we assume that DNA is from a mammal or bird but RNA comes from a virus. To study thermodynamic properties of this model, we use methods of statistical mechanics, namely, the theory of Gibbs measures. We use these measures to describe phases (states) of the DNA–RNA system. Using a Markov chain (corresponding to Gibbs measure) we give conditions (on temperature) of DNA–RNA renaturation.
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4

Haq, Ihtshamul. "Thermodynamics of drug–DNA interactions." Archives of Biochemistry and Biophysics 403, no. 1 (July 2002): 1–15. http://dx.doi.org/10.1016/s0003-9861(02)00202-3.

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5

Utsuno, Kuniharu, and Hasan Uludağ. "Thermodynamics of Polyethylenimine-DNA Binding and DNA Condensation." Biophysical Journal 99, no. 1 (July 2010): 201–7. http://dx.doi.org/10.1016/j.bpj.2010.04.016.

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6

Tsuruta, Mitsuki, Yui Sugitani, Naoki Sugimoto, and Daisuke Miyoshi. "Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes." International Journal of Molecular Sciences 22, no. 2 (January 19, 2021): 947. http://dx.doi.org/10.3390/ijms22020947.

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Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.
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7

Gutierrez, Hernan Oscar Cortez, Milton Milciades Cortez Gutierrez, Girady Iara Cortez Fuentes Rivera, Liv Jois Cortez Fuentes Rivera, and Deolinda Fuentes Rivera Vallejo. "Dark breather using symmetric Morse, solvent and external potentials for DNA breathing." Eclética Química Journal 43, no. 4 (December 5, 2018): 44. http://dx.doi.org/10.26850/1678-4618eqj.v43.4.2018.p43-48.

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We analyze the dynamics and the quantum thermodynamics of DNA in Symmetric-Peyrard-Bishop-Dauxois model (S-PBD) with solvent and external potentials and describe the transient conformational fluctuations using dark breather and the ground state wave function of the associate Schrodinger differential equation. We used the S-PBD, the Floquet theory, quantum thermodynamic and finite difference methods. We show that for lower coupling dark breather is present. We estimate the fluctuations or breathing of DNA. For the S-PBD model we have the stability of dark breather for k<0.004 and mobile breathers with coupling k=0.004. The fluctuations of the dark breather in the S-PBD model is approximately zero with the quantum thermodynamics. The viscous and external potential effect is direct proportional to hydrogen bond stretching.
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8

Gutierrez, Hernan Oscar Cortez, Milton Milciades Cortez Gutierrez, Girady Iara Cortez Fuentes Rivera, Liv Jois Cortez Fuentes Rivera, and Deolinda Fuentes Rivera Vallejo. "Dark breather using symmetric Morse, solvent and external potentials for DNA breathing." Eclética Química Journal 43, no. 4 (January 7, 2019): 44. http://dx.doi.org/10.26850/1678-4618eqj.v43.4.2018.p44-49.

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We analyze the dynamics and the quantum thermodynamics of DNA in Symmetric-Peyrard-Bishop-Dauxois model (S-PBD) with solvent and external potentials and describe the transient conformational fluctuations using dark breather and the ground state wave function of the associate Schrodinger differential equation. We used the S-PBD, the Floquet theory, quantum thermodynamic and finite difference methods. We show that for lower coupling dark breather is present. We estimate the fluctuations or breathing of DNA. For the S-PBD model we have the stability of dark breather for k<0.004 and mobile breathers with coupling k=0.004. The fluctuations of the dark breather in the S-PBD model is approximately zero with the quantum thermodynamics. The viscous and external potential effect is direct proportional to hydrogen bond stretching.
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9

Petruska, J., M. F. Goodman, M. S. Boosalis, L. C. Sowers, C. Cheong, and I. Tinoco. "Comparison between DNA melting thermodynamics and DNA polymerase fidelity." Proceedings of the National Academy of Sciences 85, no. 17 (September 1, 1988): 6252–56. http://dx.doi.org/10.1073/pnas.85.17.6252.

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10

Schmitt, Terry J., and Thomas A. Knotts. "Thermodynamics of DNA hybridization on surfaces." Journal of Chemical Physics 134, no. 20 (May 28, 2011): 205105. http://dx.doi.org/10.1063/1.3592557.

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11

SantaLucia, John, and Donald Hicks. "The Thermodynamics of DNA Structural Motifs." Annual Review of Biophysics and Biomolecular Structure 33, no. 1 (June 9, 2004): 415–40. http://dx.doi.org/10.1146/annurev.biophys.32.110601.141800.

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12

Scialdone, Antonio, and Mario Nicodemi. "DNA Loci Cross-Talk through Thermodynamics." Journal of Biomedicine and Biotechnology 2009 (2009): 1–8. http://dx.doi.org/10.1155/2009/516723.

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The recognition and pairing of specific DNA loci, though crucial for a plenty of important cellular processes, are produced by still mysterious physical mechanisms. We propose the first quantitative model from Statistical Mechanics, able to clarify the interaction allowing such “DNA cross-talk” events. Soluble molecules, which bind some DNA recognition sequences, produce an effective attraction between distant DNA loci; if their affinity, their concentration, and the relative DNA binding sites number exceed given thresholds, DNA colocalization occurs as a result of a thermodynamic phase transition. In this paper, after a concise report on some of the most recent experimental results, we introduce our model and carry out a detailed “in silico” analysis of it, by means of Monte Carlo simulations. Our studies, while rationalize several experimental observations, result in very interesting and testable predictions.
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13

Alniss, Hasan Y. "Thermodynamics of DNA Minor Groove Binders." Journal of Medicinal Chemistry 62, no. 2 (July 30, 2018): 385–402. http://dx.doi.org/10.1021/acs.jmedchem.8b00233.

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14

Sanchez, Robersy, and Sally A. Mackenzie. "Information Thermodynamics of Cytosine DNA Methylation." PLOS ONE 11, no. 3 (March 10, 2016): e0150427. http://dx.doi.org/10.1371/journal.pone.0150427.

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15

Marquet, R., and C. Houssier. "Thermodynamics of Cation-Induced DNA Condensation." Journal of Biomolecular Structure and Dynamics 9, no. 1 (August 1991): 159–67. http://dx.doi.org/10.1080/07391102.1991.10507900.

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16

Takeda, Y., P. D. Ross, and C. P. Mudd. "Thermodynamics of Cro protein-DNA interactions." Proceedings of the National Academy of Sciences 89, no. 17 (September 1, 1992): 8180–84. http://dx.doi.org/10.1073/pnas.89.17.8180.

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17

Mayama, Hiroyuki, and Kenichi Yoshikawa. "Thermodynamics in folding transition of DNA." Macromolecular Symposia 160, no. 1 (October 2000): 55–60. http://dx.doi.org/10.1002/1521-3900(200010)160:1<55::aid-masy55>3.0.co;2-t.

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18

Zhong, Min, and Neville R. Kallenbach. "Conformation and Thermodynamics of DNA "Necks"." Journal of Molecular Biology 230, no. 3 (April 1993): 766–78. http://dx.doi.org/10.1006/jmbi.1993.1199.

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19

Wang, Qian, and B. Montgomery Pettitt. "Modeling DNA Thermodynamics under Torsional Stress." Biophysical Journal 106, no. 5 (March 2014): 1182–93. http://dx.doi.org/10.1016/j.bpj.2014.01.022.

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20

Šponar, J., and H. Votavová. "Stability and thermodynamics of DNA models." Thermochimica Acta 245 (October 1994): 83–88. http://dx.doi.org/10.1016/0040-6031(94)85071-2.

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21

Goodman, M. F. "DNA replication fidelity: kinetics and thermodynamics." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 200, no. 1-2 (July 1988): 11–20. http://dx.doi.org/10.1016/0027-5107(88)90067-x.

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22

Bae, Jin H., John Z. Fang, and David Yu Zhang. "High-throughput methods for measuring DNA thermodynamics." Nucleic Acids Research 48, no. 15 (June 16, 2020): e89-e89. http://dx.doi.org/10.1093/nar/gkaa521.

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Abstract Understanding the thermodynamics of DNA motifs is important for prediction and design of probes and primers, but melt curve analyses are low-throughput and produce inaccurate results for motifs such as bulges and mismatches. Here, we developed a new, accurate and high-throughput method for measuring DNA motif thermodynamics called TEEM (Toehold Exchange Energy Measurement). It is a refined framework of comparing two toehold exchange reactions, which are competitive strand displacement between oligonucleotides. In a single experiment, TEEM can measure over 1000 ΔG° values with standard error of roughly 0.05 kcal/mol.
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23

Peterson, Jacob. "Understanding the Thermodynamics of Biological Order." American Biology Teacher 74, no. 1 (January 1, 2012): 22–24. http://dx.doi.org/10.1525/abt.2012.74.1.6.

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By growth in size and complexity (i.e., changing from more probable to less probable states), plants and animals appear to defy the second law of thermodynamics. The usual explanation describes the input of nutrient and sunlight energy into open thermodynamic systems. However, energy input alone does not address the ability to organize and create complex structures or explain life cycles – in particular, growth regulation and dying in the presence of adequate nutrients. Understanding the roles of macromolecules such as DNA, with their apparent information-processing capability, affords opportunity to understand biological order.
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24

Zerze, Gül H., Frank H. Stillinger, and Pablo G. Debenedetti. "Thermodynamics of DNA Hybridization from Atomistic Simulations." Journal of Physical Chemistry B 125, no. 3 (January 12, 2021): 771–79. http://dx.doi.org/10.1021/acs.jpcb.0c09237.

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25

Gutiérrez, Hernán Cortez, Elso Drigo Filho, José Roberto Ruggiero, Milton Cortez Gutierrez, and Liv Cortez Fuentes Rivera. "Thermodynamics of DNA with “hump” Morse potential." Eclética Química Journal 41, no. 1 (October 5, 2017): 60. http://dx.doi.org/10.26850/1678-4618eqj.v41.1.2016.p60-65.

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The thermal denaturation of DNA, i.e. the separation of the two strands is a phenomenon caused by the amplitude of the vibrations of the bases, therefore it is necessary to know how such separation is generated in order to implement alternative model of the melting behavior as a function of nucleotide sequence and therapies to combat the cancer. We propose to use the extended nonlinear Peyrard-Bishop(PB) model of DNA to include an anharmonic potential representing the aromatic stacking interaction between n- and (n-1)-th consecutive base pairs to treat the problem. We use Finite-difference methods for determine the mean value of the displacement for the “hump Morse” potential of the Peyrard-Bishop model of DNA. We show how the extended “pseudo-Schrödinger” combined with finite difference method can be used to obtain the mean value displacements for the thermal denaturation of DNA with “hump” Morse potential.
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26

Rozikov, U. A. "Thermodynamics of interacting systems of DNA molecules." Theoretical and Mathematical Physics 206, no. 2 (February 2021): 174–84. http://dx.doi.org/10.1134/s0040577921020057.

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27

Rebecca Locker, C., Stephen D. Fuller, and Stephen C. Harvey. "DNA Organization and Thermodynamics during Viral Packing." Biophysical Journal 93, no. 8 (October 2007): 2861–69. http://dx.doi.org/10.1529/biophysj.106.094771.

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28

Travers, Andrew A., and Georgi Muskhelishvili. "DNA thermodynamics shape chromosome organization and topology." Biochemical Society Transactions 41, no. 2 (March 21, 2013): 548–53. http://dx.doi.org/10.1042/bst20120334.

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How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.
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29

Li, Li. "Thermodynamics of an Asymmetric DNA Holliday Junction." BIO 1, no. 1 (February 21, 2011): 52–63. http://dx.doi.org/10.5618/bio.2011.v1.n1.2.

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30

Zoli, Marco. "Thermodynamics of twisted DNA with solvent interaction." Journal of Chemical Physics 135, no. 11 (September 21, 2011): 115101. http://dx.doi.org/10.1063/1.3631564.

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31

Allawi, H. "Thermodynamics of internal C.T mismatches in DNA." Nucleic Acids Research 26, no. 11 (June 1, 1998): 2694–701. http://dx.doi.org/10.1093/nar/26.11.2694.

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32

Müller, Susanne, Marco E. Bianchi, and Stefan Knapp. "Thermodynamics of HMGB1 Interaction with Duplex DNA†." Biochemistry 40, no. 34 (August 2001): 10254–61. http://dx.doi.org/10.1021/bi0100900.

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33

Spink, Charles H., Liang Ding, Qingyi Yang, Richard D. Sheardy, and Nadrian C. Seeman. "Thermodynamics of Forming a Parallel DNA Crossover." Biophysical Journal 97, no. 2 (July 2009): 528–38. http://dx.doi.org/10.1016/j.bpj.2009.04.054.

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34

Härd, Torleif, and Thomas Lundbäck. "Thermodynamics of sequence-specific protein-DNA interactions." Biophysical Chemistry 62, no. 1-3 (November 1996): 121–39. http://dx.doi.org/10.1016/s0301-4622(96)02197-7.

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35

Xu, Jun, and Stephen L. Craig. "Thermodynamics of DNA Hybridization on Gold Nanoparticles." Journal of the American Chemical Society 127, no. 38 (September 2005): 13227–31. http://dx.doi.org/10.1021/ja052352h.

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36

Petruska, John, and Myron F. Goodman. "Enthalpy-Entropy Compensation in DNA Melting Thermodynamics." Journal of Biological Chemistry 270, no. 2 (January 13, 1995): 746–50. http://dx.doi.org/10.1074/jbc.270.2.746.

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37

Ramprakash, Jayanthi, Brian Lang, and Frederick P. Schwarz. "Thermodynamics of single strand DNA base stacking." Biopolymers 89, no. 11 (November 2008): 969–79. http://dx.doi.org/10.1002/bip.21044.

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38

McCauley, Micah J., Caitlin J. Cain, Leah Furman, Catherine A. Dietrich, Sally Ruderman, Diana Seminario-McCormick, Grace Ferris, Megan E. Nunez, and Mark C. Williams. "Kinetics and Thermodynamics of Non-Canonical DNA." Biophysical Journal 110, no. 3 (February 2016): 407a. http://dx.doi.org/10.1016/j.bpj.2015.11.2198.

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39

AUGUSTO, Paulo Sergio Pilz, Elso DRIGO FILHO, and Jose Roberto RUGGIERO. "Statistical Model to DNA Melting." Eclética Química 26 (2001): 77–85. http://dx.doi.org/10.1590/s0100-46702001000100006.

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40

González-Amezcua, O., and M. Hernández-Contreras. "Structural thermodynamics of lamellar cationic lipid-DNA complex: DNA compressibility modulus." Journal of Chemical Physics 123, no. 22 (December 8, 2005): 224906. http://dx.doi.org/10.1063/1.2137697.

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41

Moody, Maurice R., Marcel H. P. van Genderen, and Henk M. Buck. "Thermodynamics of polymolecular duplexes between phosphate-methylated DNA and natural DNA." Biopolymers 30, no. 5-6 (1990): 609–18. http://dx.doi.org/10.1002/bip.360300513.

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42

Bates, Andrew D., Agnes Noy, Michael M. Piperakis, Sarah A. Harris, and Anthony Maxwell. "Small DNA circles as probes of DNA topology." Biochemical Society Transactions 41, no. 2 (March 21, 2013): 565–70. http://dx.doi.org/10.1042/bst20120320.

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Small DNA circles can occur in Nature, for example as protein-constrained loops, and can be synthesized by a number of methods. Such small circles provide tractable systems for the study of the structure, thermodynamics and molecular dynamics of closed-circular DNA. In the present article, we review the occurrence and synthesis of small DNA circles, and examine their utility in studying the properties of DNA and DNA–protein interactions. In particular, we highlight the analysis of small circles using atomistic simulations.
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43

Binder, Hans. "Thermodynamics of competitive surface adsorption on DNA microarrays." Journal of Physics: Condensed Matter 18, no. 18 (April 19, 2006): S491—S523. http://dx.doi.org/10.1088/0953-8984/18/18/s02.

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44

Lundbaeck, Thomas, Johanna Zilliacus, Jan-Aake Gustafsson, Jan Carlstedt-Duke, and Torleif Haerd. "Thermodynamics of sequence-specific glucocorticoid receptor-DNA interactions." Biochemistry 33, no. 19 (May 17, 1994): 5955–65. http://dx.doi.org/10.1021/bi00185a037.

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45

Deleeuw, Lynn, Anna V. Tchernatynskaia, and Andrew N. Lane. "Thermodynamics and Specificity of the Mbp1−DNA Interaction†." Biochemistry 47, no. 24 (June 2008): 6378–85. http://dx.doi.org/10.1021/bi702339q.

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46

Mascotti, David P., and Timothy M. Lohman. "Thermodynamics of Oligoarginines Binding to RNA and DNA†." Biochemistry 36, no. 23 (June 1997): 7272–79. http://dx.doi.org/10.1021/bi970272n.

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47

Li, Ying, Gerald Zon, and W. David Wilson. "Thermodynamics of DNA duplexes with adjacent G.cntdot.A mismatches." Biochemistry 30, no. 30 (July 1991): 7566–72. http://dx.doi.org/10.1021/bi00244a028.

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48

Cruz, Fernando J. A. L., and José P. B. Mota. "Conformational Thermodynamics of DNA Strands in Hydrophilic Nanopores." Journal of Physical Chemistry C 120, no. 36 (September 2, 2016): 20357–67. http://dx.doi.org/10.1021/acs.jpcc.6b06234.

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49

Bullough, R. K., Yu-zhong Chen, and J. T. Timonen. "Thermodynamics of Toda lattice models: application to DNA." Physica D: Nonlinear Phenomena 68, no. 1 (September 1993): 83–92. http://dx.doi.org/10.1016/0167-2789(93)90032-v.

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50

Dauxois, Thierry, Michel Peyrard, and A. R. Bishop. "Thermodynamics of a nonlinear model for DNA denaturation." Physica D: Nonlinear Phenomena 66, no. 1-2 (June 1993): 35–42. http://dx.doi.org/10.1016/0167-2789(93)90221-l.

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