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Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2021-10-25 , DOI: 10.1021/acs.jpcb.1c05598 Branislav Milovanović 1 , Milena Petković 1 , Igor Popov 2, 3 , Mihajlo Etinski 1
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2021-10-25 , DOI: 10.1021/acs.jpcb.1c05598 Branislav Milovanović 1 , Milena Petković 1 , Igor Popov 2, 3 , Mihajlo Etinski 1
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Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation–cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines’ carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.
中文翻译：
水介导的相互作用增强了 DNA 四链体中胞嘧啶四重体相邻空腔中的碱土阳离子螯合
与单价对应物相比，二价阳离子之间更大的库仑排斥决定了四链体中央离子通道中的阳离子-阳离子距离。在这项工作中，采用密度泛函理论和连续溶剂化模型来研究碱土阳离子在中心离子通道相邻空腔中的键能。研究了蛋白质数据库中可用的具有各种几何约束和结构基序的四种结晶四分子四链体，以了解如何在水溶液中增加阳离子结合亲和力。与鸟嘌呤和尿嘧啶四重体相比，夹在鸟嘌呤四重体之间的胞嘧啶四重体具有更大的第二碱土阳离子键能。与鸟嘌呤的羰基相比，胞嘧啶四重体中心的四个高度保守的氢键水分子与阳离子具有更高的静电相互作用。报告的发现对于设计用于光电应用的以二价阳离子为模板的合成四链体很有价值。
更新日期：2021-11-04
中文翻译：
水介导的相互作用增强了 DNA 四链体中胞嘧啶四重体相邻空腔中的碱土阳离子螯合
与单价对应物相比，二价阳离子之间更大的库仑排斥决定了四链体中央离子通道中的阳离子-阳离子距离。在这项工作中，采用密度泛函理论和连续溶剂化模型来研究碱土阳离子在中心离子通道相邻空腔中的键能。研究了蛋白质数据库中可用的具有各种几何约束和结构基序的四种结晶四分子四链体，以了解如何在水溶液中增加阳离子结合亲和力。与鸟嘌呤和尿嘧啶四重体相比，夹在鸟嘌呤四重体之间的胞嘧啶四重体具有更大的第二碱土阳离子键能。与鸟嘌呤的羰基相比，胞嘧啶四重体中心的四个高度保守的氢键水分子与阳离子具有更高的静电相互作用。报告的发现对于设计用于光电应用的以二价阳离子为模板的合成四链体很有价值。
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