Single-molecule studies of RNA aptamers binding to SARS-CoV-2 spike proteins expressed on virus-like particles.

Abstract

The SARS-CoV-2 spike protein is the responsible agent for the first step of viral entry into human cells. We present single-molecule total internal reflection fluorescence studies of fluorescently tagged RNA aptamers designed to bind to the receptor binding domain (RBD) of the spike protein, neutralizing its ability to bind to the ACE-2 receptor. Our results show individual binding and unbinding events of aptamers, which are recorded as a function of time. An analysis of these single-molecule trajectories indicates that multiple aptamers can bind to the spike trimer with high affinity, and that aptamers are able to bind spike proteins on virus-like particles. This single-molecule approach allows new insights into ligand binding to multimeric proteins and viruses. We show that multivalent interactions increase the affinity of RNA aptamers to the spike protein in both the wild-type and Omicron SARS-CoV-2 variants.