Molecular dynamic simulation of the thermodynamic and kinetic properties of nucleotide base pair

doi:10.1088/1674-1056/26/12/128705

Abstract

A nucleotide base pair is the basic unit of RNA structures. Understanding the thermodynamic and kinetic properties of the closing and opening of a base pair is vital for quantitative understanding the biological functions of many RNA molecules. Due to the fast transition rate, it is difficult to directly observe opening and closing of single nucleic acid base pair in experiments. This review will provide a brief summary of the studies about the thermodynamic and kinetic properties of a base pair opening and closing by using molecular dynamic simulation methods.

Keywords: thermodynamics kinetics molecular dynamic simulation

Received: 29 August 2017
Revised: 14 October 2017
Accepted manuscript online:

PACS:	87.10.Tf	(Molecular dynamics simulation)
	87.14.gn	(RNA)
	87.15.ap	(Molecular dynamics simulation)
	87.15.Cc	(Folding: thermodynamics, statistical mechanics, models, and pathways)

Fund:

Project supported by the National Natural Science Foundation of China (Grant Nos. 11574234 and 31270761).

Corresponding Authors: Wen-Bing Zhang
E-mail: wbzhang@whu.edu.cn

Cite this article:

Yu-Jie Wang(王宇杰), Zhen Wang(王珍), Yan-Li Wang(王晏莉), Wen-Bing Zhang(张文炳) Molecular dynamic simulation of the thermodynamic and kinetic properties of nucleotide base pair 2017 Chin. Phys. B 26 128705

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