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Advance in Structural Bioinformatics pp 187–203Cite as

Binding Modes and Interaction Mechanism Between Different Base Pairs and Methylene Blue Trihydrate: A Quantum Mechanics Study

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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 827))

Abstract

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.

Huiying Chu, Jinguang Wang and Peijun Xu have been contributed equally to this paper.

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Authors and Affiliations

  1. School of Physics and Electronic Technology, Liaoning Normal University, Dalian, Liaoning, China

    Peijun Xu, Depeng Zhang, Meixia Zhao & Jiahui Liu

  2. The First Affiliated Hospital, Dalian Medical University, Dalian, China

    Jinguang Wang

  3. Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China

    Huiying Chu, Hujun Shen & Guohui Li

  4. Guangzhou Institute of Biomedicine and Health, Guangzhou, China

    Yong Xu

Authors
  1. Peijun Xu
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  2. Jinguang Wang
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  3. Yong Xu
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  4. Huiying Chu
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Correspondence to Guohui Li .

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Editors and Affiliations

  1. Shanghai JiaoTong University, Shanghai, China

    Dongqing Wei

  2. Shanghai Jiao Tong University, Shanghai, China

    Qin Xu

  3. Shanghai Jiao Tong University, Shanghai, China

    Tangzhen Zhao

  4. Shanghai Jiao Tong University, Shanghai, China

    Hao Dai

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© 2015 Shanghai Jiaotong University Press, Shanghai and Springer Science+Business Media Dordrecht

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Xu, P. et al. (2015). Binding Modes and Interaction Mechanism Between Different Base Pairs and Methylene Blue Trihydrate: A Quantum Mechanics Study. In: Wei, D., Xu, Q., Zhao, T., Dai, H. (eds) Advance in Structural Bioinformatics. Advances in Experimental Medicine and Biology, vol 827. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9245-5_12

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