A MOLECULAR-DYNAMICS SIMULATION OF THE (DG)6.(DC)6 MINIHELIX INCLUDING COUNTERIONS AND WATER

被引：21

作者：

ZIELINSKI, TJ ^{[1
]}

SHIBATA, M ^{[1
]}

机构：

[1] NEW YORK STATE DEPT HLTH, ROSWELL PK MEM INST, DEPT BIOPHYS, BUFFALO, NY 14263 USA

来源：

BIOPOLYMERS | 1990年 / 29卷 / 6-7期

关键词：

D O I：

10.1002/bip.360290614

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The results of a 60 ps molecular dynamics (MD) simulation of (dG)6·(dC)6 including 10 Na+ counterions and 292 water molecules are presented. All backbone angles and helix parameters for the hexamer are reported in this paper along with trajectory plots of selected angles. Hydrogen bonding between the bases along the helical axis was observed to flucturate with time, showing the dynamic nature of the base‐pairing interaction. These fluctuations gave rise to unusual hydrogen‐bonding patterns. Good intrastrad base stacking and no interstrand base stacking were also observed. The hexamer minihelix retains an essentially B‐DNA conformation throughout the entire simulation even though some helix parameters and backbone angles do not have strict B‐DNA values. The most striking feature obtained from the simulation was a high propeller twist, which resulted in a narrow minor groove for the minihelix. It is proposed that (dG)n·(dC)n sequences are resistant to DNAase I because of this narrow minor groove in dilute aqueous solution. Copyright © 1990 John Wiley & Sons, Inc.

引用

页码：1027 / 1044

页数：18

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