Malysheva Daria O, Dymova Maya A, Richter Vladimir A
Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia.
Physics Department, Novosibirsk State University, Novosibirsk, Russia.
Biophys Rev. 2024 Nov 20;16(6):685-700. doi: 10.1007/s12551-024-01252-z. eCollection 2024 Dec.
Aptamers are short oligonucleotides that bind specifically to various ligands and are characterized by their low immunogenicity, thermostability, and ease of labeling. Many biomedical applications of aptamers as biosensors and drug delivery agents are currently being actively researched. Selective affinity selection with exponential ligand enrichment (SELEX) allows to discover aptamers for a specific target, but it only provides information about the sequence of aptamers; hence other approaches are used for determining aptamer structure, aptamer-ligand interactions and the mechanism of action. The first one is in silico modelling that allows to infer likely secondary and tertiary structures and model their interactions with a ligand. The second approach is to use instrumental methods to study structure and aptamer-ligand interaction. In silico modelling and instrumental methods are complimentary and their combined use allows to eliminate some ambiguity in their respective results. This review examines both the advantages and limitations of in silico modelling and instrumental approaches currently used to study aptamers, which will allow researchers to develop optimal study designs for analyzing aptamer structure and ligand interactions.
适体是能特异性结合各种配体的短寡核苷酸，其特点是免疫原性低、热稳定性高且易于标记。目前，适体作为生物传感器和药物递送剂的许多生物医学应用正在积极研究中。指数富集配体的系统进化技术（SELEX）允许发现针对特定靶标的适体，但它仅提供适体序列的信息；因此，需要使用其他方法来确定适体结构、适体-配体相互作用及作用机制。第一种方法是计算机模拟，它可以推断可能的二级和三级结构，并对它们与配体的相互作用进行建模。第二种方法是使用仪器方法来研究结构和适体-配体相互作用。计算机模拟和仪器方法是相辅相成的，它们的联合使用可以消除各自结果中的一些模糊性。本综述探讨了目前用于研究适体的计算机模拟和仪器方法的优点和局限性，这将有助于研究人员为分析适体结构和配体相互作用制定最佳研究设计。
