Reconfiguration of B-DNA structure induced by ethanol

doi:10.1088/1674-1056/adbed9

中国物理B ›› 2025, Vol. 34 ›› Issue (8): 88707-088707.doi: 10.1088/1674-1056/adbed9

所属专题： SPECIAL TOPIC — A celebration of the 90th Anniversary of the Birth of Bolin Hao

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

收稿日期:2024-11-11 修回日期:2025-02-13 接受日期:2025-03-11 出版日期:2025-07-17 发布日期:2025-07-17
通讯作者: Rongri Tan, Huanhuan Qiu E-mail:rogertanr@hotmail.com;qiu.hhhh@126.com
基金资助:
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).

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

Received:2024-11-11 Revised:2025-02-13 Accepted:2025-03-11 Online:2025-07-17 Published:2025-07-17
Contact: Rongri Tan, Huanhuan Qiu E-mail:rogertanr@hotmail.com;qiu.hhhh@126.com
Supported by:
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).

摘要/Abstract

摘要： 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.

关键词: ethanol, molecular dynamic simulation, DNA configuration

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.

Key words: ethanol, molecular dynamic simulation, DNA configuration

中图分类号: (DNA)

87.14.gk

87.15.ap (Molecular dynamics simulation) 87.15.-v (Biomolecules: structure and physical properties) 87.15.hp (Conformational changes)

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[J]. 中国物理B, 2025, 34(8): 88707-088707.

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[J]. Chin. Phys. B, 2025, 34(8): 88707-088707.

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Reconfiguration of B-DNA structure induced by ethanol

Reconfiguration of B-DNA structure induced by ethanol

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