Electric Field of DNA in Solution: Who Is in Charge?,Physical Review X

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Electric Field of DNA in Solution: Who Is in Charge?
Physical Review X ( IF 11.6 ) Pub Date : 2024-09-05 , DOI: 10.1103/physrevx.14.031042
Jonathan G. Hedley ₁ , Kush Coshic ₂ , Aleksei Aksimentiev ₂ , Alexei A. Kornyshev _{1,

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Affiliation

In solution, DNA, the “most important molecule of life,” is a highly charged macromolecule that bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions (cations of the solution) adsorbed at or condensed near it, DNA still produces a substantial electric field in its vicinity, which is screened by buffer electrolytes at longer distances from the DNA. This electric field is experienced by any charged or dipolar species approaching and interacting with the DNA. So far, such a field has been explored predominantly within the scope of a primitive model of the electrolytic solution, not considering more complicated structural effects of the water solvent. In this paper, we investigate the distribution of electric field around DNA using linear response nonlocal electrostatic theory, applied here for helix-specific charge distributions, and compare the predictions of such a theory with specially performed, fully atomistic, large-scale, molecular dynamics simulations. Both approaches are applied to unravel the role of the structure of water at close distances to and within the grooves of a DNA molecule in the formation of the electric field. As predicted by the theory and reported by the simulations, the main finding of this study is that oscillations in the electrostatic potential distribution are present around DNA, caused by the overscreening effect of structured water. Surprisingly, electrolyte ions at physiological concentrations do not strongly disrupt these oscillations and are rather distributed according to these oscillating patterns, indicating that water structural effects dominate the short-range electrostatics. We also show that (i) structured water adsorbed in the grooves of DNA leads to a positive electrostatic potential core relative to the bulk, (ii) the Debye length some 10 Å away from the DNA surface is reduced, effectively renormalized by the helical pitch of the DNA molecule, and (iii) Lorentzian contributions to the nonlocal dielectric function of water, effectively reducing the dielectric constant close to the DNA surface, enhance the overall electric field. The impressive agreement between the atomistic simulations and the developed theory substantiates the use of nonlocal electrostatics when considering solvent effects in molecular processes in biology.

Published by the American Physical Society

2024

中文翻译：

溶液中 DNA 的电场：谁负责？

在溶液中，DNA 是“生命中最重要的分子”，是一种带高电荷的大分子，其糖磷酸骨架的每个磷酸盐上都带有一个负电荷单位。尽管 DNA 被吸附或在其附近冷凝的反离子（溶液的阳离子）部分补偿，但 DNA 仍然在其附近产生大量电场，该电场被距离 DNA 较远的缓冲电解质筛选。任何带电或偶极物质接近 DNA 并与之相互作用时都会经历这种电场。到目前为止，这样的领域主要在电解液的原始模型范围内进行探索，没有考虑水溶剂更复杂的结构效应。在本文中，我们使用线性响应非局部静电理论研究 DNA 周围电场的分布，该理论在这里应用于螺旋特异性电荷分布，并将这种理论的预测与专门执行的、完全原子化的、大规模的分子动力学模拟进行了比较。这两种方法都用于揭示 DNA 分子凹槽附近和内部水的结构在电场形成中的作用。正如理论预测和模拟报告的那样，本研究的主要发现是 DNA 周围存在静电电位分布的振荡，这是由结构水的过度筛选效应引起的。令人惊讶的是，生理浓度的电解质离子并没有强烈破坏这些振荡，而是根据这些振荡模式分布，这表明水的结构效应在短程静电中占主导地位。我们还表明，（i）吸附在 DNA 凹槽中的结构水导致相对于本体的正静电电位核心，（ii）距离 DNA 表面约 10 Å 的德拜长度减少，被 DNA 分子的螺旋间距有效地重新标准化，以及（iii）洛伦兹对水的非局部介电功能的贡献，有效降低靠近DNA表面的介电常数，增强整体电场。原子模拟和发展的理论之间令人印象深刻的一致性证实了在考虑生物学分子过程中的溶剂效应时使用非局部静电。美国物理学会 2024 年出版

更新日期：2024-09-05

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