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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
关键词MD simulations isonucleosidep backbone helix parameter thermal stability
刊名JOURNAL OF MOLECULAR MODELING
2006-09-01
DOI10.1007/s00894-005-0085-8
12期:6页:781-791
收录类别SCI
文章类型Article
WOS标题词Science & Technology
类目[WOS]Biochemistry & Molecular Biology ; Biophysics ; Chemistry, Multidisciplinary ; Computer Science, Interdisciplinary Applications
研究领域[WOS]Biochemistry & Molecular Biology ; Biophysics ; Chemistry ; Computer Science
关键词[WOS]PARTICLE MESH EWALD ; HUMAN-IMMUNODEFICIENCY-VIRUS ; NUCLEIC-ACIDS ; CONTINUUM SOLVENT ; FREE-ENERGIES ; A-DNA ; OLIGONUCLEOTIDES ; STABILITY ; PHOSPHOROTHIOATE ; PARAMETERS
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.

语种英语
WOS记录号WOS:000240900700005
引用统计
被引频次:6[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/61793
专题北京大学药学院
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.
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