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

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 dir...

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Published inChinese physics B Vol. 26; no. 12; pp. 1 - 6
Main Author 王宇杰;王珍;王晏莉;张文炳
Format Journal Article
LanguageEnglish
Published 01.12.2017
Online AccessGet full text
ISSN1674-1056
2058-3834
DOI10.1088/1674-1056/26/12/128705

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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.
AbstractList 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.
Author 王宇杰;王珍;王晏莉;张文炳
AuthorAffiliation Department of Physics, Wuhan University, Wuhan 430071, China;Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466000, China
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Cites_doi 10.1021/ja408595e
10.1021/ar9500933
10.1146/annurev.biochem.77.061206.174353
10.1073/pnas.1517511113
10.1063/1.1630572
10.1021/ja210531q
10.1021/ja5100756
10.1529/biophysj.105.078774
10.1103/RevModPhys.62.251
10.1016/j.tig.2005.03.007
10.1021/bi00202a022
10.1021/ja0470721
10.1093/nar/gkg239
10.1006/jmbi.1999.3001
10.1146/annurev.physchem.59.032607.093743
10.1021/ja00007a023
10.1146/annurev-biochem-060713-035524
10.1073/pnas.221593598
10.1002/bip.22331
10.1021/j100324a007
10.1093/nar/gkp834
10.1016/j.mib.2007.03.003
10.1016/j.sbi.2004.04.001
10.1016/S0022-2836(02)00194-8
10.1093/nar/gkg835
10.1016/j.bpj.2012.03.074
10.4161/epi.20170
10.1529/biophysj.104.045179
10.1146/annurev.biophys.37.032807.125957
10.1002/(ISSN)1521-3773
10.1073/pnas.0901178106
10.1073/pnas.2036378100
10.1021/bi9809425
10.1038/nsmb763
10.1093/nar/gkg941
10.1093/nar/gkv570
10.1038/nature07348
10.1021/bi00119a005
10.1038/nature10885
10.1021/ja1109425
10.1021/ja025980x
10.1016/j.str.2006.09.002
10.1017/S1355838299990805
10.1002/cbic.v7:3
10.1016/S0166-1280(96)04974-3
10.1146/annurev.biophys.37.032807.130000
10.1063/1.4944067
10.1093/nar/gnf057
10.1016/j.cbpa.2008.09.017
10.1021/bi010385d
10.1073/pnas.0702137104
10.1038/nature12649
10.1038/35103511
10.1261/rna.2253310
10.1021/ja9743497
10.1016/0076-6879(89)80108-9
10.1021/ct500120v
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Notes Yu-Jie Wang1,2, Zhen Wang1, Yan-Li Wang1, Wen-Bing Zhang1（1. Department of Physics, Wuhan University, Wuhan 430071, China;2. Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466000, China）
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.
thermodynamics; kinetics; molecular dynamic simulation
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References 44
45
46
47
48
49
Bao L (35) 2016; 25
50
51
52
53
10
54
11
55
12
56
13
57
14
58
15
59
16
Qi W P (33) 2011; 28
17
18
19
Li Z C (34) 2015; 32
1
2
3
4
5
6
7
8
9
60
20
21
22
23
24
25
26
27
28
29
30
31
32
36
37
38
39
40
41
42
43
References_xml – volume: 25
  issn: 1674-1056
  year: 2016
  ident: 35
  publication-title: Chin. Phys.
– ident: 12
  doi: 10.1021/ja408595e
– ident: 14
  doi: 10.1021/ar9500933
– ident: 18
  doi: 10.1146/annurev.biochem.77.061206.174353
– ident: 42
  doi: 10.1073/pnas.1517511113
– ident: 52
  doi: 10.1063/1.1630572
– ident: 45
  doi: 10.1021/ja210531q
– ident: 9
  doi: 10.1021/ja5100756
– ident: 25
  doi: 10.1529/biophysj.105.078774
– ident: 51
  doi: 10.1103/RevModPhys.62.251
– ident: 3
  doi: 10.1016/j.tig.2005.03.007
– ident: 26
  doi: 10.1021/bi00202a022
– ident: 41
  doi: 10.1021/ja0470721
– ident: 43
  doi: 10.1093/nar/gkg239
– ident: 6
  doi: 10.1006/jmbi.1999.3001
– ident: 10
  doi: 10.1146/annurev.physchem.59.032607.093743
– ident: 44
  doi: 10.1021/ja00007a023
– ident: 20
  doi: 10.1146/annurev-biochem-060713-035524
– ident: 27
  doi: 10.1073/pnas.221593598
– ident: 55
  doi: 10.1002/bip.22331
– ident: 50
  doi: 10.1021/j100324a007
– ident: 58
  doi: 10.1093/nar/gkp834
– ident: 16
  doi: 10.1016/j.mib.2007.03.003
– ident: 46
  doi: 10.1016/j.sbi.2004.04.001
– ident: 37
  doi: 10.1016/S0022-2836(02)00194-8
– ident: 49
  doi: 10.1093/nar/gkg835
– ident: 23
  doi: 10.1016/j.bpj.2012.03.074
– ident: 1
  doi: 10.4161/epi.20170
– ident: 24
  doi: 10.1529/biophysj.104.045179
– ident: 17
  doi: 10.1146/annurev.biophys.37.032807.125957
– ident: 31
  doi: 10.1002/(ISSN)1521-3773
– ident: 53
  doi: 10.1073/pnas.0901178106
– ident: 39
  doi: 10.1073/pnas.2036378100
– volume: 32
  issn: 0256-307X
  year: 2015
  ident: 34
  publication-title: Chin. Phys. Lett.
– ident: 47
  doi: 10.1021/bi9809425
– ident: 7
  doi: 10.1038/nsmb763
– ident: 40
  doi: 10.1093/nar/gkg941
– ident: 60
  doi: 10.1093/nar/gkv570
– ident: 2
  doi: 10.1038/nature07348
– ident: 5
  doi: 10.1021/bi00119a005
– volume: 28
  issn: 0256-307X
  year: 2011
  ident: 33
  publication-title: Chin. Phys. Lett.
– ident: 19
  doi: 10.1038/nature10885
– ident: 59
  doi: 10.1021/ja1109425
– ident: 38
  doi: 10.1021/ja025980x
– ident: 11
  doi: 10.1016/j.str.2006.09.002
– ident: 15
  doi: 10.1017/S1355838299990805
– ident: 32
  doi: 10.1002/cbic.v7:3
– ident: 36
  doi: 10.1016/S0166-1280(96)04974-3
– ident: 8
  doi: 10.1146/annurev.biophys.37.032807.130000
– ident: 48
  doi: 10.1063/1.4944067
– ident: 30
  doi: 10.1093/nar/gnf057
– ident: 29
  doi: 10.1016/j.cbpa.2008.09.017
– ident: 22
  doi: 10.1021/bi010385d
– ident: 28
  doi: 10.1073/pnas.0702137104
– ident: 54
  doi: 10.1038/nature12649
– ident: 4
  doi: 10.1038/35103511
– ident: 13
  doi: 10.1261/rna.2253310
– ident: 56
  doi: 10.1021/ja9743497
– ident: 21
  doi: 10.1016/0076-6879(89)80108-9
– ident: 57
  doi: 10.1021/ct500120v
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