Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
Phys Chem Chem Phys. 2023 Oct 18;25(40):27744-27755. doi: 10.1039/d3cp02606j.
Double-stranded DNA bears the highest linear negative charge density (2 per base-pair) among all biopolymers, leading to strong interactions with cations and dipolar water, resulting in the formation of a dense 'condensation layer' around DNA. Interactions involving proteins and ligands binding to DNA are primarily governed by strong electrostatic forces. Increased salt concentrations impede such electrostatic interactions - a situation that prevails in oceanic species due to their cytoplasm being enriched with salts. Nevertheless, how these interactions' dynamics are affected in crowded hypersaline environments remains largely unexplored. Here, we employ steady-state and time-resolved fluorescence Stokes shifts (TRFSS) of a DNA-bound ligand (DAPI) to investigate the static and dynamic solvation properties of DNA in the presence of two divalent cations, magnesium (Mg), and calcium (Ca) at varying high to very-high concentrations of 0.15 M, 1 M and 2 M. We compare the results to those obtained in physiological concentrations (0.15 M) of monovalent Na ions. Combining data from fluorescence femtosecond optical gating (FOG) and time-correlated single photon counting (TCSPC) techniques, dynamic fluorescence Stokes shifts in DNA are analysed over a broad range of time-scales, from 100 fs to 10 ns. We find that while divalent cation crowding strongly influences the DNA stability and ligand binding affinity to DNA, the dynamics of DNA solvation remain remarkably similar across a broad range of five decades in time, even in a high-salinity crowded environment with divalent cations, as compared to the physiological concentration of the Na ion. Steady-state and time-resolved data of the DNA-groove-bound ligand are seemingly unaffected by ion-crowding in hypersaline solution, possibly due to ions being mostly displaced by the DNA-bound ligand. Furthermore, the dynamic coupling of cations with nearby water may possibly contribute to a net-neutral effect on the overall collective solvation dynamics in DNA, owing to the strong anti-correlation of their electrostatic interaction energy fluctuations. Such dynamic scenarios may persist within the cellular environment of marine life and other biological cells that experience hypersaline conditions.
双链 DNA 具有所有生物聚合物中最高的线性负电荷密度（每碱基对 2 个），导致其与阳离子和偶极水分子强烈相互作用，从而在 DNA 周围形成致密的“凝聚层”。涉及与 DNA 结合的蛋白质和配体的相互作用主要受强静电相互作用的控制。增加盐浓度会阻碍这种静电相互作用——这种情况在海洋物种中普遍存在，因为它们的细胞质富含盐分。然而，在拥挤的高盐环境中，这些相互作用的动力学如何受到影响在很大程度上仍未得到探索。在这里，我们使用与 DNA 结合的配体（DAPI）的稳态和时间分辨荧光斯托克斯位移（TRFSS）来研究在两种二价阳离子镁（Mg）和钙（Ca）存在下，DNA 的静态和动态溶剂化性质在不同高至非常高的浓度为 0.15 M、1 M 和 2 M。我们将结果与在生理浓度（0.15 M）的单价 Na 离子下获得的结果进行比较。结合荧光飞秒光门（FOG）和时间相关单光子计数（TCSPC）技术的数据，在从 100 fs 到 10 ns 的广泛时间尺度上分析 DNA 的动态荧光斯托克斯位移。我们发现，尽管二价阳离子拥挤强烈影响 DNA 的稳定性和配体与 DNA 的结合亲和力，但在广泛的五个时间尺度范围内，DNA 溶剂化的动力学仍然非常相似，即使在具有二价阳离子的高盐拥挤环境中，与 Na 离子的生理浓度相比也是如此。在高盐溶液中，似乎离子拥挤对 DNA 沟槽结合配体的稳态和时间分辨数据没有影响，这可能是由于离子主要被 DNA 结合配体取代。此外，阳离子与附近水分子的动态耦合可能对 DNA 整体集体溶剂化动力学产生净中性效应，这是由于它们的静电相互作用能波动呈强烈反相关。这种动态情况可能在海洋生物和其他经历高盐条件的生物细胞的细胞环境中持续存在。
