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长程 DNA-水相互作用。

Long-range DNA-water interactions.

机构信息

Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia.

Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia.

出版信息

Biophys J. 2021 Nov 16;120(22):4966-4979. doi: 10.1016/j.bpj.2021.10.016. Epub 2021 Oct 21.

Abstract

DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.

摘要

DNA 仅在水相环境中发挥功能,其构象会随水合水平的变化而改变。水合作用会导致水分子的动态变化,从而产生旋转和振荡的偶极子,进而在兆赫兹到太赫兹波段产生强烈的吸收。然而,由于水在兆赫兹到太赫兹频率范围内的强吸收,研究水合作用对 DNA 动力学和受 DNA 影响的水分子光谱特征的影响极具挑战性。针对这一问题,我们采用了高精度兆赫兹到太赫兹介电谱仪,并结合分子动力学模拟,研究了 DNA 水合壳层内水分子的动力学以及水合 DNA 的集体振动运动,这些对于 DNA 的构象和功能至关重要。研究结果表明,DNA 溶液中水分子的动力学是不均匀的,表现出四个不同弛豫时间的层次结构,范围从约 8 ps 到 1 ns,并且 DNA 链的水合结构可以延伸到离其表面约 18 Å 的距离。已经鉴定出了水合 DNA 的低频集体振动模式,并且发现它们对环境条件(包括温度和水合水平)敏感。这些结果揭示了水合 DNA 动力学和 DNA-水界面的关键信息,这些信息影响 DNA 的生化功能和反应性。

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