Nucleic acid base pair dynamics: The impact of sequence and structure using free-energy calculations

被引:42
作者
Giudice, E [1 ]
Lavery, R [1 ]
机构
[1] CNRS, UPR 9080, Inst Biol Physicochim, Lab Biochim Theor, F-75005 Paris, France
关键词
D O I
10.1021/ja034095r
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Molecular dynamics free-energy calculations of base pair opening within double helical DNA and RNA are used to explain why A-tracts (oligo-adenine repeats) greatly increase the lifetimes of AT base pairs, whereas the structural and the chemical changes involved in passing from B-DNA to A-RNA have comparatively small effects. Copyright © 2003 American Chemical Society.
引用
收藏
页码:4998 / 4999
页数:2
相关论文
共 18 条
[1]   Free energy and structural pathways of base flipping in a DNA GCGC containing sequence [J].
Banavali, NK ;
MacKerell, AD .
JOURNAL OF MOLECULAR BIOLOGY, 2002, 319 (01) :141-160
[2]  
Case DA, 1999, AMBER 6
[4]   ... THE TYRANNY OF THE LATTICE ... [J].
DICKERSON, RE ;
GOODSELL, DS ;
NEIDLE, S .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (09) :3579-3583
[5]   ON THE SEQUENCE DETERMINANTS AND FLEXIBILITY OF THE KINETOPLAST DNA FRAGMENT WITH ABNORMAL GEL-ELECTROPHORETIC MOBILITIES [J].
DIEKMANN, S ;
WANG, JC .
JOURNAL OF MOLECULAR BIOLOGY, 1985, 186 (01) :1-11
[6]   SEQUENCE DEPENDENCE OF BASE-PAIR OPENING IN A DNA DODECAMER CONTAINING THE CACA/GTGT SEQUENCE MOTIF [J].
FOLTASTOGNIEW, E ;
RUSSU, IM .
BIOCHEMISTRY, 1994, 33 (36) :11016-11024
[7]   Base pair opening within B-DNA:: free energy pathways for GC and AT pairs from umbrella sampling simulations [J].
Giudice, E ;
Várnai, P ;
Lavery, R .
NUCLEIC ACIDS RESEARCH, 2003, 31 (05) :1434-1443
[8]  
Giudice E, 2001, CHEMPHYSCHEM, V2, P673, DOI 10.1002/1439-7641(20011119)2:11<673::AID-CPHC673>3.0.CO
[9]  
2-S
[10]  
Gueron M, 1995, METHOD ENZYMOL, V261, P383