Theoretical Investigation of the structure and Raman scattering properties of Hoogsteen- and Watson-Crick-type Adenine-Thymine base pair

IF 2 3区化学 Q4 CHEMISTRY, PHYSICAL

Chemical Physics Pub Date : 2024-09-19 DOI:10.1016/j.chemphys.2024.112465

Yu Xiao , Feng-Yi Zhang , Ming-Jun Ma , Si-Jun Lu , Yong-Jun Zhang , Xiao-Yu Zhao , Ya-Xin Wang , Kun Zhang , Hong-Liang Xu

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Abstract

Hoogsteen (HG) and Watson-Crick (WC) adenine–thymine (A-T) base pairs are fundamental to gene expression and genomic stability. Our research applied density functional theory (DFT) calculations to analyze these base pairs, demonstrating that linking them with ribose or deoxyribose and their immersion in solvents markedly enhances the distinctions in their optical properties. DFT results reveal that N···HN hydrogen bonds in both HG and WC pairs exhibit characteristics of both ionic and covalent bonds, playing a crucial role in their stability. While WC base pairs demonstrate stronger orbital interactions, they also experience greater repulsion than HG pairs. This repulsion offsets the positive interactions to a degree, making the interaction energy of WC pairs slightly lower than that of HG pairs. Furthermore, the distinct conformations of these base pairs result in different vibrational modes, suggesting Raman spectroscopy as an effective method for distinguishing between WC and HG base pairs.

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胡格斯坦和沃森-克里克型腺嘌呤-酪氨酸碱基对的结构和拉曼散射特性的理论研究

Hoogsteen（HG）和 Watson-Crick （WC）腺嘌呤-胸腺嘧啶（A-T）碱基对是基因表达和基因组稳定性的基础。我们的研究运用密度泛函理论（DFT）计算来分析这些碱基对，结果表明，将它们与核糖或脱氧核糖连接起来并浸入溶剂中，能显著增强它们的光学特性差异。DFT 结果表明，HG 和 WC 碱基对中的 N-HN 氢键同时具有离子键和共价键的特征，对它们的稳定性起着至关重要的作用。虽然 WC 碱基对表现出更强的轨道相互作用，但它们也比 HG 碱基对具有更大的斥力。这种斥力在一定程度上抵消了正相互作用，使得 WC 碱基对的相互作用能略低于 HG 碱基对。此外，这些碱基对的不同构象导致了不同的振动模式，这表明拉曼光谱是区分 WC 和 HG 碱基对的有效方法。

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来源期刊

Chemical Physics 化学-物理：原子、分子和化学物理

CiteScore

4.60

自引率

4.30%

发文量

278

审稿时长

39 days

期刊介绍： Chemical Physics publishes experimental and theoretical papers on all aspects of chemical physics. In this journal, experiments are related to theory, and in turn theoretical papers are related to present or future experiments. Subjects covered include: spectroscopy and molecular structure, interacting systems, relaxation phenomena, biological systems, materials, fundamental problems in molecular reactivity, molecular quantum theory and statistical mechanics. Computational chemistry studies of routine character are not appropriate for this journal.