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Heterogeneous hydration patterns of G-quadruplex DNA |
| Cong-Min Ji(祭聪敏), Yusong Tu(涂育松), and Yuan-Yan Wu(吴园燕)† |
| College of Physics Science and Technology, Yangzhou University, Yangzhou 225009, China |
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Abstract G-quadruplexes (GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. Their structure and function are strongly influenced by their hydration shells. Although extensively studied through various experimental and computational methods, hydration patterns near DNA remain under debate due to the chemically and topologically heterogeneous nature of the exposed surface. In this work, we employed all-atom molecular dynamics (MD) simulation to study the hydration patterns of GQ DNA. The Drude oscillator model was used in MD simulation as a computationally efficient method for modeling electronic polarization in DNA ion solutions. Hydration structure was analyzed in terms of radial distribution functions and high-density three-dimensional hydration sites. Analysis of hydration dynamics focused on self-diffusion rates and orientation time correlation at different structural regions of GQ DNA. The results show highly heterogeneous hydration patterns in both structure and dynamics; for example, there are several insular high-density sites in the inner channel, and ‘spine of water’ in the groove. For water inside the loop, anomalous diffusion is present over a long time scale, but for water around the phosphate group and groove, diffusion becomes normal after ～ 30 ps. These essentially correspond to deeply buried structural water and strong interaction with DNA, respectively.
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Received: 21 March 2022
Revised: 11 May 2022
Accepted manuscript online: 29 May 2022
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PACS:
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87.14.gk
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(DNA)
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87.15.-v
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(Biomolecules: structure and physical properties)
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87.15.ag
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(Quantum calculations)
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87.15.ap
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(Molecular dynamics simulation)
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| Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11705160 and 11647074). |
Corresponding Authors:
Yuan-Yan Wu
E-mail: yywu@yzu.edu.cn
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Cite this article:
Cong-Min Ji(祭聪敏), Yusong Tu(涂育松), and Yuan-Yan Wu(吴园燕) Heterogeneous hydration patterns of G-quadruplex DNA 2023 Chin. Phys. B 32 028702
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