<i>In silico</i> strategies for modeling RNA aptamers and predicting binding sites of their molecular targets

RNA aptamers are single-stranded nucleic acids of 20–100 nucleotides, with high sensitivity and specificity against particular molecular targets. <i>In vitro</i> production and selection of aptamers can be performed using the SELEX method. However, this procedure requires considerable time and cost. In this sense, bioinformatics tools play an important role in reducing the time and cost associated with development and production of aptamers. In this article, we propose bioinformatics strategies for modeling and analysis of the interaction with molecular targets for two RNA aptamers: ATP binding RNA aptamer and iSpinach aptamer. For this purpose, molecular modeling of the tertiary structure of the aptamers was performed with two servers (SimRNA and RNAComposer); and AutoDock Vina and rDock programs were used to dock their respective ligands. The predictions developed with these methods could be used for <i>in silico</i> design of RNA aptamers, through a simple and accessible methodology. Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.1951754 .RNA适配体（RNA aptamers）是一类长度为20~100个核苷酸的单链核酸，对特定分子靶点具有高灵敏度与特异性。体外（in vitro）适配体的制备与筛选可通过指数富集配体系统进化（SELEX）技术完成，但该流程需耗费大量时间与成本。有鉴于此，生物信息学工具对于降低适配体开发与生产的相关时间及成本具有重要作用。本文针对两种RNA适配体——ATP结合型RNA适配体与iSpinach适配体，提出了用于其与分子靶点相互作用建模及分析的生物信息学策略。为此，研究人员借助两款服务器（SimRNA与RNAComposer）完成了适配体三级结构的分子建模，并通过AutoDock Vina与rDock程序对各自的配体进行分子对接。通过上述方法得到的预测结果，可依托简便易行的方法用于RNA适配体的计算机模拟（in silico）设计。本文的补充数据可通过以下在线链接获取：https://doi.org/10.1080/15257770.2021.1951754。