Selection of FANA Aptamers to Inhibit Sars-CoV-2 Infection

Abstract

Aptamers are short nucleic acid sequences that bind to a particular protein target. Recently, FANA aptamers have been found to be ideal subjects for therapeutic treatments of SARS-CoV-2 as they are highly specific, resistant to degradation, and have low immunogenicity. Previous research has identified a FANA aptamer that binds to the receptor binding domain (RBD) of the SARS-CoV-2 Wuhan strain, blocking infection in an airway epithelium model. However, past research has also revealed the possibility of an aptamer that binds to the S1 subunit of SARS-CoV-2 and blocks infection, even without binding directly to the RBD. Thus, our research is focused on identifying FANA aptamers that bind tightly to the SARS-CoV-2 XBB.1.5 variant’s S1 subunit, with the potential to block viral infection. We identified these aptamers by following the systematic evolution of ligands by exponential enrichment (SELEX) protocol, which involves synthesizing FANA start material, isolating sequences that bind to the protein target using magnetic bead assays, performing PCR reactions, and repeating selection cycles until we have selected for aptamers with tight binding affinity. After 7 selection cycles, we identified 32 potential aptamer sequences using Sanger Sequencing and compared their properties. We found that FANA-R7-17 bound very tightly to XBB.1.5-S1 with a Kd of 46 ± 15 pM, and had a half-life of about 21 minutes. Among all the aptamers we compared, FANA-R7-17 presents the greatest potential as an aptamer to the SARS-CoV-2 XBB.1.5 variant, though future research would need to be conducted to determine its ability to block infection in a human airway epithelium model.