Computational Simulation of Aptamer-target Binding Mechanisms  

适配体-靶标结合机制的计算模拟

作　　者：YANG Yuan-Yuan XU Fei WU Xiu-Xiu 杨园媛;徐斐;吴秀秀(上海理工大学健康科学与工程学院,上海食品快速检测工程技术研究中心,上海200093)

机构地区：[1]School of Health Science and Engineering,University of Shanghai for Science and Technology,Shanghai Engineering Research Center of Food Rapid Detection,Shanghai 200093,China

出　　处：《中国生物化学与分子生物学报》2024年第11期1550-1562,共13页Chinese Journal of Biochemistry and Molecular Biology

基　　金：国家自然科学基金(No.32072312)资助。

摘　　要：Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as biochemical sensors for medicine,food safety and environmental monitoring.However,there is little research on aptamer-target binding mechanisms,which limits their application and development.Computational simulation has gained much attention for revealing aptamer-target binding mechanisms at the atomic level.This work summarizes the main simulation methods used in the mechanistic analysis of aptamer-target complexes,the characteristics of binding between aptamers and different targets(metal ions,small organic molecules,biomacromolecules,cells,bacteria and viruses),the types of aptamer-target interactions and the factors influencing their strength.It provides a reference for further use of simulations in understanding aptamer-target binding mechanisms.适配体是一种单链寡聚核苷酸,可与靶标特异性结合,具有制备简单、易于修饰、结构稳定和可重复使用等优点,在医药、食品安全和环境监测等领域的生化传感检测方面有良好的应用前景。目前,对适配体与靶标结合机制的了解相对匮乏,这严重限制了其应用研究和发展。计算模拟方法因在微观水平上解析适配体与靶标结合机制的优势,逐渐受到关注。本文概述了计算模拟在适配体-靶标复合物机制解析中的主要方法,总结了适配体与金属离子、有机小分子、生物大分子、细胞、细菌、病毒等不同靶标之间的结合特点,阐述了适配体-靶标间的各种相互作用力类型及影响其强弱的因素,可为计算模拟在适配体-靶标结合机制的应用研究提供借鉴和参考。

关 键 词：computational simulation APTAMER TARGET binding mechanism intermolecular forces 

分 类 号：O643.12[理学—物理化学] TP391.9[理学—化学]