Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations
文献类型：期刊论文
| 作者 | Jin, Hongwei; Zheng, Suxin; Wang, Zhanli; Luo, Cheng ; Shen, Jianhua; Jiang, Hualiang; Zhang, Liangren; Zhang, Lihe
|
| 刊名 | JOURNAL OF MOLECULAR MODELING
 |
| 出版日期 | 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 |
| WOS记录号 | WOS:000240900700005 |
| 出版者 | SPRINGER |
| 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. |
入库方式： OAI收割
来源：上海药物研究所
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