In Vitro Selection of VHH Antibodies That Recognize the Tertiary Structure of Single-Stranded DNA Aptamers

Background: DNA–protein interactions form crucial intermolecular systems in biological processes such as transcriptional regulation. The best-known DNA–protein interactions typically involve double-stranded DNA, but single-stranded DNA–binding proteins (SSBs) also exist in nature. Moreover, there are protein-binding DNA aptamers: artificially created single-stranded DNA molecules obtained through in vitro selection to target specific proteins. However, little research has used in vitro selection to identify proteins that recognize the tertiary structure formed by single-stranded DNA. Most research has focused on using DNA libraries for in vitro selection of target proteins. Methods: In this study, we performed in vitro selection using the cDNA display method and a VHH library of single-domain antibodies to determine the tertiary structure of a DNA aptamer that binds to the antibiotic oxytetracycline (OTC). We also used AlphaFold to predict the binding of VHH to DNA aptamers. Results: Our results suggest that the interaction depends on the aptamer’s structural characteristics. While relatively high association rates were observed regardless of the presence or absence of OTC, the dissociation rate was lower in the OTC (+) condition. Conclusions: These findings suggest that there may be proteins that recognize the tertiary structure of nucleic acids, in addition to those that bind to double-stranded DNA.