Base flipping in DNA:: Pathways and energetics studied with molecular dynamic simulations

被引：67

作者：

Várnai, P ^{[1
]}

Lavery, R ^{[1
]}

机构：

[1] CNRS, UPR 9080, Inst Biol Phys Chim, Lab Biochim Theor, F-75005 Paris, France

来源：

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY | 2002年 / 124卷 / 25期

关键词：

D O I：

10.1021/ja025980x

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Carrying out chemistry on the bases of DNA, necessary for biological processes such as methylation or repair, requires flipping the base into an accessible position. In this work, molecular dynamics simulations are used to generate a free energy profile for flipping a cytosine base out of its helical stack in double-stranded DNA. The results shed light on the mechanics of this process by comparing routes for base flipping via the minor and major grooves. Copyright © 2002 American Chemical Society.

引用

页码：7272 / 7273

页数：2

共 18 条

[1]

BANAVALI NK, IN PRESS J MOL BIOL

[2] Modelling base pair opening: the role of helical twist [J].

Bernet, J ;

Zakrzewska, K ;

Lavery, R .

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 1997, 398 :473-482

[3] CONSTANT-TEMPERATURE FREE-ENERGY SURFACES FOR PHYSICAL AND CHEMICAL PROCESSES [J].

BOCZKO, EM ;

BROOKS, CL .

JOURNAL OF PHYSICAL CHEMISTRY, 1993, 97 (17) :4509-4513

[4]

Case DA, 1999, AMBER 6

[5] Spontaneous base flipping in DNA and its possible role in methyltransferase binding [J].

Chen, YZ ;

Mohan, V ;

Griffey, RH .

PHYSICAL REVIEW E, 2000, 62 (01) :1133-1137

[6] AdoMet-dependent methylation, DNA methyltransferases and base flipping [J].

Cheng, XD ;

Roberts, RJ .

NUCLEIC ACIDS RESEARCH, 2001, 29 (18) :3784-3795

[7]

Giudice E, 2001, CHEMPHYSCHEM, V2, P673, DOI 10.1002/1439-7641(20011119)2:11<673::AID-CPHC673>3.0.CO

[8]

2-S

[9]

Gueron M, 1995, METHOD ENZYMOL, V261, P383

[10] Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution [J].

Klimasauskas, S ;

Szyperski, T ;

Serva, S ;

Wüthrich, K .

EMBO JOURNAL, 1998, 17 (01) :317-324

← 1 2 →