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

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.