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题名: Binding Modes and Interaction Mechanism Between Different Base Pairs and Methylene Blue Trihydrate: A Quantum Mechanics Study
作者: Xu, Peijun1;  Wang, Jinguang2;  Xu, Yong3;  Chu, Huiying4;  Shen, Hujun4;  Zhang, Depeng1;  Zhao, Meixia1;  Liu, Jiahui1;  Li, Guohui4;  Wei, D;  Xu, Q;  Zhao, T;  Dai, H
关键词: DNA base pairs ;  Intercalators methylene blue trihydrate ;  Quantum mechanic methods ;  Charge density
刊名: ADVANCE IN STRUCTURAL BIOINFORMATICS
发表日期: 2015
DOI: 10.1007/978-94-017-9245-5_12
卷: 827, 页:187-203
收录类别: BSCI ;  SCI
文章类型: Article
WOS标题词: Science & Technology ;  Life Sciences & Biomedicine
类目[WOS]: Mathematical & Computational Biology ;  Medical Informatics
研究领域[WOS]: Mathematical & Computational Biology ;  Medical Informatics
英文摘要: Different quantum mechanic methods have been evaluated for the calculation of binding modes and interactions between intercalators with different DNA base pairs by comparing with the results of MP2, which is very expensive, indicating that WB97XD method under 6-311+G* basis set is able to efficiently reproduce MP2 results. We discovered that the methylene blue trihydrate intercalated into the DNA base pairs, and DNA intercalation increased the distance between DNA base pairs, depending on the types of DNA bases. According to the binding energy results, it was found that the intercalation of methylene blue trihydrate into AA-TT base pair was more favorable in the orientation of nitrogen than other directions and intercalation, and the electric charge was transferred from methylene blue trihydrate to the AA-TT base pair. The analysis of change in the charge density shows that changes often take place in the heavy atom in the middle of the system which the charge density changes most remarkable.
关键词[WOS]: DENSITY-FUNCTIONAL THEORY ;  STACKING INTERACTIONS ;  DNA ;  INTERCALATION ;  PARAMETERS ;  MOLECULES ;  ETHIDIUM ;  EXCHANGE
语种: 英语
WOS记录号: WOS:000350428600013
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/146040
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Liaoning Normal Univ, Sch Phys & Elect Technol, Dalian, Liaoning, Peoples R China
2.Dalian Med Univ, Affiliated Hosp 1, Dalian, Peoples R China
3.Guangzhou Inst Biomed & Hlth, Guangzhou, Guangdong, Peoples R China
4.Chinese Acad Sci, Dalian Inst Chem Phys, Lab Mol Modeling & Design, State Key Lab Mol React Dynam, Dalian, Liaoning, Peoples R China

Recommended Citation:
Xu, Peijun,Wang, Jinguang,Xu, Yong,et al. Binding Modes and Interaction Mechanism Between Different Base Pairs and Methylene Blue Trihydrate: A Quantum Mechanics Study[J]. ADVANCE IN STRUCTURAL BIOINFORMATICS,2015,827:187-203.
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