Comparative Characterization of Diverse DNA Aptamers for Recognition of Spike Proteins of Multiple SARS-CoV-2 Variants

Many DNA aptamers have been reported to target the spike protein (S-protein) of SARS-CoV-2. These aptamers display different affinities or recognize different epitopes of the S-protein. We conducted a comparative study of 9 DNA aptamers for binding to several variants of the S-protein and pseudoviruses using the same testing methods, including dot-blot assays and enzyme-linked aptamer binding assays, to evaluate their affinity ranking and analytical utility. Moreover, the binding sites of these aptamers on the S-protein were examined using aptamer competition assays to understand the effect of S-protein mutations on aptamer affinity and the degree of overlapping of the binding sites by these aptamers.