Development of RNA Aptamers That Inhibit the RNA-Dependent RNA Polymerase Activity of SARS-CoV-2 Strains In Vitro

The continuous emergence of SARS-CoV-2 variants with enhanced transmissibility and immune escape capability underscores the urgent need for mutation-independent anti-viral strategies. SARS-CoV-2 non-structural protein 12 (NSP12), which encodes the RNA-dependent RNA polymerase (RdRp), is an essential component of the viral replication complex and represents a highly conserved target for therapeutic intervention. In this study, we developed RNA aptamers, composed of 2′-hydroxyl nucleotides or 2′-fluoro pyrimidines, targeting NSP12 using the SELEX (Systematic Evolution of Ligands by EXponential enrichment) approach. SELEX was performed with purified NSP12 protein derived from the Omicron variant, leading to the identification of aptamer candidates with high binding ability. RNA–protein pull-down assays confirmed binding between representative aptamers and NSP12 with high affinity. Competition assays supported binding specificity between aptamers and NSP12. Of note, functional evaluation using a primer extension assay revealed that the aptamers effectively inhibited NSP12 RdRp activity in vitro. Furthermore, the aptamers consistently bound to and inhibited NSP12 variants from wild-type, Alpha, Delta, and Omicron strains. These results suggest that the selected RNA aptamers are potential as broad-spectrum inhibitors targeting a conserved region of NSP12 and may serve as a promising platform for the development of anti-viral agents against current and emerging SARS-CoV-2 variants, as well as other RNA viruses.