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| SPECIAL TOPIC — A celebration of the 90th Anniversary of the Birth of Bolin Hao |
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Reconfiguration of B-DNA structure induced by ethanol |
| Yue Huang(黄悦)†, Yipeng Chen(陈以鹏)†, Jing Li(李静), Rongri Tan(谈荣日)‡, and Huanhuan Qiu(邱环环)§ |
| Department of Physics, Jiangxi Science and Technology Normal University, Nanchang 330038, China |
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Abstract Solution environment can influence the flexible structure of DNA under specific conditions, thereby affecting the stability of nucleic acids and ultimately impacting critical biological processes such as replication and transcription. Intracellular solution environment is variable, and previous studies have demonstrated that it can enhance the stability of DNA structures under certain circumstances. In this work, molecular dynamics simulations were conducted on B-DNA (1ZEW, with a nucleotide sequence of CCTCTAGAGG) derived from human breast cancer cells (MDA-MB231) to explore the effects of ethanol solution on DNA configuration transformation at different temperatures and concentrations. The calculated results indicate that ethanol facilitates the transition of 1ZEW from B-DNA to A-DNA at lower temperature. Furthermore, it is observed that temperature affects DNA structure to some extent, thereby modifying the trend in DNA configuration transformation. At low temperatures, the ethanol can promote the transformation of B-DNA into A-DNA at higher concentrations. While at higher temperatures, the DNA could be in a state of thermal melting. These conclusions presented here can give valuable insights into how ethanol affects B-DNA configuration transformations.
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Received: 11 November 2024
Revised: 13 February 2025
Accepted manuscript online: 11 March 2025
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PACS:
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87.14.gk
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(DNA)
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87.15.ap
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(Molecular dynamics simulation)
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87.15.-v
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(Biomolecules: structure and physical properties)
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87.15.hp
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(Conformational changes)
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| Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 52073128 and 11964012) and the Foundation of Educational Committee of Jiangxi Province of China (Grant No. GJJ2201314). |
Corresponding Authors:
Rongri Tan, Huanhuan Qiu
E-mail: rogertanr@hotmail.com;qiu.hhhh@126.com
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Cite this article:
Yue Huang(黄悦), Yipeng Chen(陈以鹏), Jing Li(李静), Rongri Tan(谈荣日), and Huanhuan Qiu(邱环环) Reconfiguration of B-DNA structure induced by ethanol 2025 Chin. Phys. B 34 088707
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[1] Mukherjee S K, Gautam S, Biswas S, Kundu J and Chowdhury P K 2015 J. Phys. Chem. B 119 14145
[2] Sarkar M, Li C and Pielak G J 2013 Biophys. Rev. 5 187
[3] Buldyrev S, Goldberger A, Havlin S, Mantegna R, Matsa M, Peng C K, Simons M and Stanley H 1995 Phys. Rev. E 51 5084
[4] Richter K, Nessling M and Lichter P 2007 J. Cell. Sci. 120 1673
[5] Richter K, Nessling M and Lichter P 2008 BBA Mol. Cell Res. 1783 2100
[6] Akabayov B and Richardson C C 2012 Biophys. J. 102 281
[7] Norred S E, Caveney P M, Chauhan G, Collier L K, Collier C P, Abel S M and Simpson M L 2018 ACS Synth. Biol. 7 1251
[8] Kong J W, Dou S X, Li W, Li H and Wang P Y 2023 Chin. Phys. Lett. 40 078701
[9] Zhang S H, Niu X Z, Wang X Z, Qu C, An H L, Zhao T J and Zhan Y 2023 Chin. Phys. B 32 050504
[10] Putzel G G, Tagliazucchi M and Szleifer I 2014 Phys. Rev. Lett. 113 138302
[11] Wang F, Baquero D P, Beltran L C, Su Z, Osinski T, Zheng W, Prangishvili D, Krupovic M and Egelman E H 2020 Proc. Natl. Acad. Sci. USA 117 19643
[12] Castaneda N, Lee M, Rivera-Jacquez H J, Marracino R R, Merlino T R and Kang H 2019 J. Phys. Chem. B 123 2770
[13] Lai C T and Schatz G C 2018 J. Phys. Chem. B 122 7990
[14] Yao F, Peng X, Su Z, Tian L, Guo Y and Kang X f 2020 Anal. Chem. 92 3827
[15] Ghosh S, Takahashi S, Ohyama T, Endoh T, Tateishi-Karimata H and Sugimoto N 2020 Proc. Natl. Acad. Sci. USA 117 14194
[16] Shet S M, Bharadwaj P, Bisht M, PereiraM M, Thayallath S K, Lokesh V, Franklin G, Kotrappanavar N S and Mondal D 2022 Int. J. Biol. Macromol. 215 184
[17] Deng Z, Prem C and Fenfei L 2023 J. Biol. Chem. 299 105439
[18] Kumar J A, Rakesh S, Preeti P and Pradipta B 2018 Plos One 13 e0206359
[19] Zhang N, Li M R, Xu H T and Zhang F S 2020 Chin. Phys. Lett. 37 088701
[20] Shim A R, Nap R J, Huang K, Almassalha L M, Matusda H, Backman V and Szleifer I 2020 Biophys. J. 118 2117
[21] Khoshbin Z, Housaindokht M R, Izadyar M, Bozorgmehr M R and Verdian A 2020 Mol. Simul. 46 592
[22] Hong F, Schreck J S and Sulc P 2020 Nucleic Acids Res. 48 10726
[23] Xue J J, Li X P, Tan R R and Zong W J 2022 Chin. Phys. B 31 048702
[24] Xue J, Wang P, Li X, Tan R and Zong W 2022 Biophys. Chem. 288 106845
[25] Hays F A, Teegarden A, Jones Z J, Harms M, Raup D, Watson J, Cavaliere E and Ho P S 2005 Proc. Natl. Acad. Sci. USA 102 7157
[26] Li J, Xie S, Zhang B, He W, Zhang Y, Wang J and Yang L 2024 Crit. Rev. Eukaryot. Gene. Expr. 34 11
[27] Mondal S, Mondal T K, Rajesh Y, Mandal M and Sinha C 2018 Polyhedron 151 344
[28] Mark P and Nilsson L 2002 J. Phys. Chem. B 106 9440
[29] Berendsen H J, Grigera J R and Straatsma T P 1987 J. Phys. Chem. C 91 6269
[30] Abraham M J, Murtola T, Schulz R, Páll S, Smith J C, Hess B and Lindahl E 2015 Softw. X 1–2 19
[31] Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis J L, Dror R O and Shaw D E 2010 Proteins 78 1950
[32] Darden T, York D and Pedersen L 1993 J. Chem. Phys. 99 10089
[33] Lavery R, Moakher M, Maddocks J H, Petkeviciute D and Zakrzewska K 2009 Nucleic Acids Res. 37 5917
[34] Li S, Olson W K and Lu X J 2019 Nucleic Acids Res. 47 W26
[35] Markham N R and Zuker M 2005 Nucleic Acids Res. 33 W577
[36] Calladine C 1982 J. Mol. Biol. 161 343
[37] Stofer E and Lavery R 1994 Biopolymers 34 337
[38] El Hassan M and Calladine C 1998 J. Mol. Biol. 282 331
[39] Zhang H, Fu H, Shao X, Dehez F, Chipot C and Cai W 2019 J. Chem. Inf. Model. 59 2324
[40] Messelson M 1958 Proc. Natl. Acad. Sci. USA 44 671
[41] Mergny J L and Lacroix L 2003 Oligonucleotides 13 515
[42] Steiner T 2002 Angew. Chem. Int. Ed. 41 48
[43] Tolokh I S, Pabit S A, Katz A M, Chen Y, Drozdetski A, Baker N, Pollack L and Onufriev A V 2014 Nucleic Acids Res. 42 10823
[44] Kirkwood J G and Boggs E M 1942 J. Chem. Phys. 10 394
[45] Wu Y Y, Zhang Z L, Zhang J S, Zhu X L and Tan Z J 2015 Nucleic Acids Res. 43 6156 |
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