TY - JOUR

T1 - Analyzing aptamer structure and interactions: in silico modelling and instrumental methods

AU - Malysheva, Daria O.

AU - Dymova, Maya A.

AU - Richter, Vladimir A.

N1 - This study was supported by the Russian Science Foundation grant No. 22–64-00041, Available online: https://rscf.ru/en/project/22-64-00041/ (accessed on 18 September 2024).

PY - 2024/11/20

Y1 - 2024/11/20

N2 - 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.

AB - 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.

KW - Ab initio modelling

KW - Aptamers

KW - Computational modelling

KW - NMR spectroscopy

KW - SAXS

KW - Structural bioinformatics

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85209668034&origin=inward&txGid=16a19138185bd2c65e1162138de08697

UR - https://www.webofscience.com/wos/woscc/full-record/WOS:001359297900001

UR - https://www.mendeley.com/catalogue/770535fc-1061-3bd8-8771-33168b29d6b7/

U2 - 10.1007/s12551-024-01252-z

DO - 10.1007/s12551-024-01252-z

M3 - Article

JO - Biophysical Reviews

JF - Biophysical Reviews

SN - 1867-2450

ER -