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The Influence of Sequence Dependence and External Solvents on DNA Conformation

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Soft Matter Systems for Biomedical Applications

Part of the book series: Springer Proceedings in Physics ((SPPHY,volume 266))

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Abstract

DNA sequence has important biological significance, its effect on groove size affects the expression of protein specific and non-specific binding groove. In liquid environments, different solvents interact with DNA differently. In this chapter, we will focus on the microscopic mechanism of internal bases and external solvents on DNA conformation. In the ordinary water solvent, with the increase of G base content, the DNA structure is transformed by B form—(A-B)—A form. In glycol solvents, DNA maintains B-form configuration, while in ethanol solvent and low activity water solvent, DNA exhibits a shorter and denser A-form.

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Abbreviations

EG:

glycol

EA:

ethanol

RDF:

radial distribution function

RMSD:

Mean square root coordinate deviation

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Acknowledgements

Thanks to Prof. L. Bulavin, N. Atamas, and K. Cherevko for the fruitful discussions. This work was supported by the National Natural Science Foundation of China under Grants No. 11635003, No.11025524, No. 11161130520, the National Basic Research Program of China under Grant No. 2010CB832903, and the European Commission’s 7th Framework Programme (Fp7-PEOPLE-2010-IRSES) under Grant Agreement Project No. 269131.

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Authors and Affiliations

  1. The Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing, 100875, China

    Hui-Ting Xu, Nan Zhang, Ming-Ru Li & Feng-Shou Zhang

  2. Beijing Radiation Center, Beijing, 100875, China

    Hui-Ting Xu, Nan Zhang, Ming-Ru Li & Feng-Shou Zhang

  3. Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou, 730000, China

    Feng-Shou Zhang

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  1. Hui-Ting Xu
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  2. Nan Zhang
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  3. Ming-Ru Li
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  4. Feng-Shou Zhang
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Correspondence to Feng-Shou Zhang .

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Editors and Affiliations

  1. Taras Shevchenko National University of Kyiv, Kyiv, Ukraine

    Leonid Bulavin

  2. National Academy of Science of Ukraine, Biocolloidal Chemistry Institute named after F.D. Ovharenko, Kyiv, Ukraine

    Nikolai Lebovka

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Xu, HT., Zhang, N., Li, MR., Zhang, FS. (2022). The Influence of Sequence Dependence and External Solvents on DNA Conformation. In: Bulavin, L., Lebovka, N. (eds) Soft Matter Systems for Biomedical Applications. Springer Proceedings in Physics, vol 266. Springer, Cham. https://doi.org/10.1007/978-3-030-80924-9_7

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