Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments

doi:10.1088/1674-1056/24/11/118701

中国物理B ›› 2015, Vol. 24 ›› Issue (11): 118701-118701.doi: 10.1088/1674-1056/24/11/118701

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

Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments

蒋杨伟^a, 冉诗勇^b, 何林李^b, 王向红^{b c}, 章林溪^a

a Department of Physics, Zhejiang University, Hangzhou 310027, China;
b Department of Physics, Wenzhou University, Wenzhou 325035, China;
c Department of Electrical and Electronic Engineering, Wenzhou Vocational and Technical College, Wenzhou 325035, China

收稿日期:2015-03-15 修回日期:2015-06-05 出版日期:2015-11-05 发布日期:2015-11-05
通讯作者: Wang Xiang-Hong E-mail:wxh@wzvtc.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant No. 31340026), the Natural Science Foundation of Zhejiang Province, China (Grant Nos. Z13F20019 and LQ12E01003), and the Science and Technology Project of Zhejiang Science and Technology Department, China (Grant No. 2014C31147).

Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments

Jiang Yang-Wei (蒋杨伟)^a, Ran Shi-Yong (冉诗勇)^b, He Lin-Li (何林李)^b, Wang Xiang-Hong (王向红)^{b c}, Zhang Lin-Xi (章林溪)^a

a Department of Physics, Zhejiang University, Hangzhou 310027, China;
b Department of Physics, Wenzhou University, Wenzhou 325035, China;
c Department of Electrical and Electronic Engineering, Wenzhou Vocational and Technical College, Wenzhou 325035, China

Received:2015-03-15 Revised:2015-06-05 Online:2015-11-05 Published:2015-11-05
Contact: Wang Xiang-Hong E-mail:wxh@wzvtc.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 31340026), the Natural Science Foundation of Zhejiang Province, China (Grant Nos. Z13F20019 and LQ12E01003), and the Science and Technology Project of Zhejiang Science and Technology Department, China (Grant No. 2014C31147).

摘要/Abstract

摘要： Using molecular dynamics simulations and atomic force microscopy (AFM), we study the decondensation process of DNA chains induced by multivalent cations at high salt concentrations in the presence of short cationic chains in solutions. The typical simulation conformations of DNA chains with varying salt concentrations for multivalent cations imply that the concentration of salt cations and the valence of multivalent cations have a strong influence on the process of DNA decondensation. The DNA chains are condensed in the absence of salt or at low salt concentrations, and the compacted conformations of DNA chains become loose when a number of cations and anions are added into the solution. It is explicitly demonstrated that cations can overcompensate the bare charge of the DNA chains and weaken the attraction interactions between the DNA chains and short cationic chains at high salt concentrations. The condensation-decondensation transitions of DNA are also experimentally observed in mixing spermidine with λ-phage DNA at different concentrations of NaCl/MgCl₂ solutions.

关键词: DNA decondensation, salt concentration, multivalent cations, molecular dynamics simulation

Abstract: Using molecular dynamics simulations and atomic force microscopy (AFM), we study the decondensation process of DNA chains induced by multivalent cations at high salt concentrations in the presence of short cationic chains in solutions. The typical simulation conformations of DNA chains with varying salt concentrations for multivalent cations imply that the concentration of salt cations and the valence of multivalent cations have a strong influence on the process of DNA decondensation. The DNA chains are condensed in the absence of salt or at low salt concentrations, and the compacted conformations of DNA chains become loose when a number of cations and anions are added into the solution. It is explicitly demonstrated that cations can overcompensate the bare charge of the DNA chains and weaken the attraction interactions between the DNA chains and short cationic chains at high salt concentrations. The condensation-decondensation transitions of DNA are also experimentally observed in mixing spermidine with λ-phage DNA at different concentrations of NaCl/MgCl₂ solutions.

Key words: DNA decondensation, salt concentration, 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)

蒋杨伟, 冉诗勇, 何林李, 王向红, 章林溪. Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments[J]. 中国物理B, 2015, 24(11): 118701-118701.

Jiang Yang-Wei (蒋杨伟), Ran Shi-Yong (冉诗勇), He Lin-Li (何林李), Wang Xiang-Hong (王向红), Zhang Lin-Xi (章林溪). Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments[J]. Chin. Phys. B, 2015, 24(11): 118701-118701.

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Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments

Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments

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