Selection and characterization of ssDNA aptamers targeting tick-borne encephalitis virus particles

Aptamers are single-stranded nucleic acids that bind to target molecules with high affinity, serving as versatile molecular tools for diagnostic and therapeutic applications. Although several aptamers against the envelope (E) protein of tick-borne encephalitis virus (TBEV) have been reported, their recognition of native viral particles remain insufficiently characterized. We identified novel ssDNA aptamers against TBEV through systematic evolution of ligands by exponential enrichment (SELEX) using a recombinant E protein that preserved the major antigenic properties of viral particles. The four major aptamer candidates showed binding activity not only to TBEV E proteins but also to TBEV-derived subviral particles. Additionally, these aptamers recognized TBEV-infected cells and retained their binding activity under serum conditions mimicking the in vivo environment. Some aptamers also exhibited inhibitory effects against TBEV infection in vitro. Furthermore, sequence truncation yielded optimized variants that retained high target affinity, demonstrated enhanced serum stability over 24 h, and neutralized viral infection. These findings provide crucial functional validation of ssDNA aptamers targeting TBEV particles and support their development as antibody-independent platforms for diagnostic, antiviral, and targeted delivery strategies for TBEV and related flaviviruses.