In vitro Selection of High Affinity DNA and RNA Aptamers that Detect Hepatitis C Virus Core Protein of Genotypes 1 to 4 and Inhibit Virus Production in Cell Culture

• DOI: 10.1016/j.jmb.2022.167501
• Publication Date: 2022-02-17T15:57:44Z
• Authors: Beatriz Torres-Vá...; Ana María de Lucas; Carlos García-Crespo; Juan Antonio Garc...; Adrián Fragoso; María Fernández-A...; Celia Perales; Esteban Domingo; Miguel Moreno; Carlos Briones
• Keywords: Aptamer; Viral protein

Hepatitis C virus (HCV) core is a highly conserved and multifunctional protein that forms the viral capsid, making it an attractive target for HCV detection inhibition. Aptamers are in vitro selected, single-stranded nucleic acids (RNA or ssDNA) with growing applicability diagnostics therapy. We have carried out DNA RNA selection against six different variants of protein: two versions full-length genotype 1, hydrophilic domain genotypes 1 to 4. The aptamer populations obtained were analyzed by means Ultra-Deep Sequencing (UDS), most abundant sequences identified number represented sequence motifs unveiled. Affinity (measured as dissociation constant, Kd) aptamers quantified using Enzyme-Linked OligoNucleotide Assay (ELONA)-based methods. Some nanomolar subnanomolar Kd values (as low 0.4 nM) common outcome selections variants. They tested sandwich competitive biosensor assays, reaching limit 2 pM. Additionally, prevalent high affinity assayed Huh-7.5 reporter cell lines infected HCV, where they decreased both progeny titer extracellular level, while increasing amount intracellular RNA. Our results suggest these inhibit capsid assembly virion formation, thus them good candidate molecules design novel therapeutic approaches hepatitis C.