Dopamine interaction with DNA/RNA aptamers: Molecular dynamics simulation

IF 3 3区化学 Q3 CHEMISTRY, PHYSICAL Computational and Theoretical Chemistry Pub Date : 2024-11-19 DOI:10.1016/j.comptc.2024.114990

Majid Sharifian, Tahereh Heidari, Mohammad Razmkhah, Fatemeh Moosavi

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Abstract

One method for detecting dopamine involves the use of RNA and DNA aptamers. Aptamers are single-stranded sequences of DNA or RNA that bind with high affinity to specific target molecules. Various aptamers have been developed to measure dopamine, making it crucial to identify which one exhibits the strongest interaction with it. This study, for the first time, examines the interaction between dopamine and aptamers using molecular dynamics simulations. The findings reveal that all three aptamers can interact with and detect dopamine. By calculating the binding Gibbs energy (ΔG_bind) between the aptamers and dopamine, it was determined that the DNA aptamer with 44 nucleotide residues is the most selective for dopamine. Additional analyses of the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radial distribution function (RDF), and radius of gyration (R_g) which assess structural stability and fluctuations further support that this aptamer has the most effective interaction with dopamine.

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多巴胺与 DNA/RNA 合体的相互作用：分子动力学模拟

检测多巴胺的一种方法是使用 RNA 和 DNA 配合物。适配体是 DNA 或 RNA 的单链序列，能与特定目标分子产生高亲和力。目前已开发出多种用于测量多巴胺的适配体，因此确定哪种适配体与多巴胺的相互作用最强至关重要。这项研究首次利用分子动力学模拟研究了多巴胺与适配体之间的相互作用。研究结果表明，所有三种适配体都能与多巴胺相互作用并检测多巴胺。通过计算适配体与多巴胺之间的结合吉布斯能（ΔGbind），确定具有 44 个核苷酸残基的 DNA 适配体对多巴胺的选择性最强。评估结构稳定性和波动性的均方根偏差（RMSD）、均方根波动（RMSF）、径向分布函数（RDF）和回旋半径（Rg）等附加分析进一步证明了这种适配体与多巴胺的相互作用最为有效。

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来源期刊

Computational and Theoretical Chemistry CHEMISTRY, PHYSICAL-

CiteScore

4.20

自引率

10.70%

发文量

331

审稿时长

31 days

期刊介绍： Computational and Theoretical Chemistry publishes high quality, original reports of significance in computational and theoretical chemistry including those that deal with problems of structure, properties, energetics, weak interactions, reaction mechanisms, catalysis, and reaction rates involving atoms, molecules, clusters, surfaces, and bulk matter.