Deciphering the Ligand-Binding Site in a DNA Aptamer Targeting Deoxynivalenol

Abstract— Food safety is one of the primary demands of modern society. Mycotoxins are toxic metabolites of food-contaminating fungi. Fungi enter the food chain by infecting crops and irreversibly contaminate them due to the structural stability of mycotoxins. Mycotoxins are stable even at extremely high temperatures; they do not lose their activity during food processing, thus posing a threat to human health. Therefore, it is crucial to detect mycotoxins in food crops during the planting process and at the beginning of the harvest, which requires a rapid and simple detection method. One of the current solutions for this problem is aptamer-based sensors. Here, we deciphered the structure of the binding site in the developed DNA aptamer against deoxynivalenol. The binding site is formed by short single-stranded sequences at the 5′- and 3′-ends of the hairpin, with the Cyanine 3 label at 3′-end. The shortest aptamer with the affinity for deoxynivalenol was used as a recognition element in the surface-enhanced Raman spectroscopy-based sensor to detect mycotoxins in wheat crops.