Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

doi:10.1007/s00894-005-0085-8

	Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations
	Jin, Hongwei ; Zheng, Suxin ; Wang, Zhanli ; Luo, Cheng; Shen, Jianhua; Jiang, Hualiang; Zhang, Liangren ; Zhang, Lihe
刊名	JOURNAL OF MOLECULAR MODELING
	2006-09
卷号	12 期号:6 页码:781-791
关键词	MD simulations isonucleosidep backbone helix parameter thermal stability
ISSN号	1610-2940
DOI	10.1007/s00894-005-0085-8
文献子类	Article
英文摘要	Some structural insights into the conformations of the isonucleosides containing duplexes have been provided. Unrestrained molecular-dynamics simulations on 18-mer duplexes with isonucleosides incorporated at the 3'-end or in the center of one strand have been carried out with explicit solvent under periodic boundary conditions using the AMBER force field and the particle mesh Ewald method. The Watson-Crick hydrogen-bonding patterns of the duplexes studied remained intact throughout the simulation. For the modified duplexes, the changes observed in the inter-base pair parameters and backbone torsional angles were primarily localized at the isonucleoside-inserted area. All five structures studied remained in the B-form family. The decreased stacking abilities indicated by the large changes in inter-base pair parameters and the large changes in backbones made the modified duplexes show a minor thermal destabilization in comparison with native DNA. The MM_PBSA method for estimating binding free energies on two complementary strands was used. The results showed that the binding free energies of isonucleoside-incorporated DNA duplexes were lower than the native DNA duplex, which is in good agreement with experimental observations.
WOS关键词	PARTICLE MESH EWALD ; HUMAN-IMMUNODEFICIENCY-VIRUS ; NUCLEIC-ACIDS ; CONTINUUM SOLVENT ; FREE-ENERGIES ; A-DNA ; OLIGONUCLEOTIDES ; STABILITY ; PHOSPHOROTHIOATE ; PARAMETERS
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics ; Chemistry ; Computer Science
语种	英语
出版者	SPRINGER
WOS记录号	WOS:000240900700005
内容类型	期刊论文
源URL	[http://119.78.100.183/handle/2S10ELR8/273512]
专题	中国科学院上海药物研究所
通讯作者	Zhang, Lihe
作者单位	1.Peking Univ, Sch Pharmaceut Sci, Natl Res Lab Nat & Biomimet Drugs, Beijing 100083, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China
推荐引用方式 GB/T 7714	Jin, Hongwei,Zheng, Suxin,Wang, Zhanli,et al. Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations[J]. JOURNAL OF MOLECULAR MODELING,2006,12(6):781-791.
APA	Jin, Hongwei.,Zheng, Suxin.,Wang, Zhanli.,Luo, Cheng.,Shen, Jianhua.,...&Zhang, Lihe.(2006).Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations.JOURNAL OF MOLECULAR MODELING,12(6),781-791.
MLA	Jin, Hongwei,et al."Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations".JOURNAL OF MOLECULAR MODELING 12.6(2006):781-791.