Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations

doi:10.1088/1674-1056/22/9/098701

中国物理B ›› 2013, Vol. 22 ›› Issue (9): 98701-098701.doi: 10.1088/1674-1056/22/9/098701

• INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY • 上一篇下一篇

Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations

柴爱华^{a b}, 冉诗勇^c, 张冬^a, 蒋杨伟^a, 杨光参^c, 章林溪^a

a Department of Physics, Zhejiang University, Hangzhou 310027, China;
b College of Mathematics, Physics and Information Engineering, Jiaxing University, Jiaxing 314001, China;
c Department of Physics, Wenzhou University, Wenzhou 325027, China

收稿日期:2012-12-22 修回日期:2013-03-15 出版日期:2013-07-26 发布日期:2013-07-26
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 20974081, 20934004, 21174131, and 21104060) and the Zhejiang Provincial Natural Science Foundation of China (Grant No. Y4110357).

Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations

Chai Ai-Hua (柴爱华)^{a b}, Ran Shi-Yong (冉诗勇)^c, Zhang Dong (张冬)^a, Jiang Yang-Wei (蒋杨伟)^a, Yang Guang-Can (杨光参)^c, Zhang Lin-Xi (章林溪)^a

a Department of Physics, Zhejiang University, Hangzhou 310027, China;
b College of Mathematics, Physics and Information Engineering, Jiaxing University, Jiaxing 314001, China;
c Department of Physics, Wenzhou University, Wenzhou 325027, China

Received:2012-12-22 Revised:2013-03-15 Online:2013-07-26 Published:2013-07-26
Contact: Zhang Lin-Xi E-mail:lxzhang@zju.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 20974081, 20934004, 21174131, and 21104060) and the Zhejiang Provincial Natural Science Foundation of China (Grant No. Y4110357).

摘要/Abstract

摘要： The condensation of DNA induced by spermine is studied by atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics (SMD) simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA-cation complexes.

关键词: DNA condensation, multivalent cations, molecular dynamics simulation

Abstract: The condensation of DNA induced by spermine is studied by atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics (SMD) simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA-cation complexes.

Key words: DNA condensation, multivalent cations, molecular dynamics simulation

中图分类号: (Biomolecules: structure and physical properties)

87.15.-v

36.20.-r (Macromolecules and polymer molecules) 82.20.Wt (Computational modeling; simulation)

柴爱华, 冉诗勇, 张冬, 蒋杨伟, 杨光参, 章林溪. Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations[J]. 中国物理B, 2013, 22(9): 98701-098701.

Chai Ai-Hua (柴爱华), Ran Shi-Yong (冉诗勇), Zhang Dong (张冬), Jiang Yang-Wei (蒋杨伟), Yang Guang-Can (杨光参), Zhang Lin-Xi (章林溪). Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations[J]. Chin. Phys. B, 2013, 22(9): 98701-098701.

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Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations

Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations

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