Supercoiled DNA Minicircles under Double-strand Breaks

Ye-Peng Qiao; Chun-Lai Ren

doi:10.1007/s10118-024-3106-8

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Supercoiled DNA Minicircles under Double-strand Breaks

RESEARCH ARTICLE | Updated：2024-08-27

- Supercoiled DNA Minicircles under Double-strand Breaks
- Supercoiled DNA Minicircles under Double-strand Breaks
- 高分子科学（英文版） 2024年42卷第9期页码：1353-1359
- Affiliations：
  
  National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
- Author bio：
  
  chunlair@nju.edu.cn
- Funds：
  
  This work was financially supported by the National Natural Science Foundation of China (Nos. 12274212, 12347102 and 12174184). We are grateful to the High Performance Computing Center (HPCC) of Nanjing University for the numerical calculations in this study on its blade cluster system.;Electronic supplementary information (ESI) is available free of charge in the online version of this article at http://doi.org/10.1007/s10118-024-3106-8.
- DOI：10.1007/s10118-024-3106-8
  中图分类号：
- 纸质出版日期：2024-09-01，
  
  网络出版日期：2024-03-29，
  
  收稿日期：2024-01-23，
  
  修回日期：2024-02-09，
  
  录用日期：2024-02-19
- Accepted：
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Qiao, Y. P.; Ren, C. L. Supercoiled DNA minicircles under double-strand breaks. Chinese J. Polym. Sci. 2024, 42, 1353–1359

Ye-Peng Qiao, Chun-Lai Ren. Supercoiled DNA Minicircles under Double-strand Breaks[J]. Chinese Journal of Polymer Science, 2024,42(9):1353-1359.
Qiao, Y. P.; Ren, C. L. Supercoiled DNA minicircles under double-strand breaks. Chinese J. Polym. Sci. 2024, 42, 1353–1359 DOI： 10.1007/s10118-024-3106-8.

Ye-Peng Qiao, Chun-Lai Ren. Supercoiled DNA Minicircles under Double-strand Breaks[J]. Chinese Journal of Polymer Science, 2024,42(9):1353-1359. DOI： 10.1007/s10118-024-3106-8.

摘要

Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization. We employed MD simulations based on the oxDNA2 model to investigate the dynamics of supercoiled minicircular DNA under double-strand breaks with two fixed endpoints

uncovering the molecular mechanism underlying the relaxation process.

Abstract

Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization. However

the molecular mechanism underlying the relaxation process remains insufficiently explored. Here we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed endpoints. Our simulations show that the conformational changes in the DNA occur continuously

with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage site. The relaxation process is influenced not only by the separation distance between the fixed ends but also their angle. Importantly

we observe an inhibitory effect on the relaxation characterized by small angles

where short terminal loops impede DNA conformational adjustments

preserving the supercoiled structure. These findings elucidate the intricate interplay between DNA conformational change

DNA motion and intramolecular stress release

shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.

关键词

Keywords

Supercoiled DNADNA minicircleDNA relaxationoxDNA modelMD simulation

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