To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?

doi:10.1088/1674-1056/27/1/018203

中国物理B ›› 2018, Vol. 27 ›› Issue (1): 18203-018203.doi: 10.1088/1674-1056/27/1/018203

所属专题： SPECIAL TOPIC — Soft matter and biological physics

• SPECIAL TOPIC—Soft matter and biological physics • 上一篇下一篇

To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?

Gui Xiong(熊贵), Kun Xi(席昆), Xi Zhang(张曦), Zhi-Jie Tan(谭志杰)

Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China

收稿日期:2017-08-31 修回日期:2017-10-23 出版日期:2018-01-05 发布日期:2018-01-05
通讯作者: Xi Zhang, Zhi-Jie Tan E-mail:xizhang@whu.edu.cn;zjtan@whu.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11374234, 11575128, 11774272, and 11647312).

To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?

Gui Xiong(熊贵), Kun Xi(席昆), Xi Zhang(张曦), Zhi-Jie Tan(谭志杰)

Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China

Received:2017-08-31 Revised:2017-10-23 Online:2018-01-05 Published:2018-01-05
Contact: Xi Zhang, Zhi-Jie Tan E-mail:xizhang@whu.edu.cn;zjtan@whu.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11374234, 11575128, 11774272, and 11647312).

摘要/Abstract

摘要： Nucleic acids are negatively charged biomolecules, and metal ions in solutions are important to their folding structures and thermodynamics, especially multivalent ions. However, it has been suggested that the binding of multivalent ions to nucleic acids cannot be quantitatively described by the well-established Poisson-Boltzmann (PB) theory. In this work, we made extensive calculations of ion distributions around various RNA-like macroions in divalent and trivalent salt solutions by PB theory and Monte Carlo (MC) simulations. Our calculations show that PB theory appears to underestimate multivalent ion distributions around RNA-like macroions while can reliably predict monovalent ion distributions. Our extensive comparisons between PB theory and MC simulations indicate that when an RNA-like macroion gets ion neutralization beyond a “critical” value, the multivalent ion distribution around that macroion can be approximately described by PB theory. Furthermore, an empirical formula was obtained to approximately quantify the critical ion neutralization for various RNA-like macroions in multivalent salt solutions, and this empirical formula was shown to work well for various real nucleic acids including RNAs and DNAs.

关键词: nucleic acids, ion binding, Poisson-Boltzmann theory, Monte Carlo simulation

Abstract: Nucleic acids are negatively charged biomolecules, and metal ions in solutions are important to their folding structures and thermodynamics, especially multivalent ions. However, it has been suggested that the binding of multivalent ions to nucleic acids cannot be quantitatively described by the well-established Poisson-Boltzmann (PB) theory. In this work, we made extensive calculations of ion distributions around various RNA-like macroions in divalent and trivalent salt solutions by PB theory and Monte Carlo (MC) simulations. Our calculations show that PB theory appears to underestimate multivalent ion distributions around RNA-like macroions while can reliably predict monovalent ion distributions. Our extensive comparisons between PB theory and MC simulations indicate that when an RNA-like macroion gets ion neutralization beyond a “critical” value, the multivalent ion distribution around that macroion can be approximately described by PB theory. Furthermore, an empirical formula was obtained to approximately quantify the critical ion neutralization for various RNA-like macroions in multivalent salt solutions, and this empirical formula was shown to work well for various real nucleic acids including RNAs and DNAs.

Key words: nucleic acids, ion binding, Poisson-Boltzmann theory, Monte Carlo simulation

中图分类号: (Polyelectrolytes)

82.35.Rs

87.14.gn (RNA) 87.10.Rt (Monte Carlo simulations) 87.14.G- (Nucleic acids)

熊贵, 席昆, 张曦, 谭志杰. To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?[J]. 中国物理B, 2018, 27(1): 18203-018203.

Gui Xiong(熊贵), Kun Xi(席昆), Xi Zhang(张曦), Zhi-Jie Tan(谭志杰). To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?[J]. Chin. Phys. B, 2018, 27(1): 18203-018203.

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To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?

To what extent of ion neutralization can multivalent ion distributions around RNA-like macroions be described by Poisson-Boltzmann theory?

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