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

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Ruiting Sun¹, Rugiya Alieva², Sergey Belousov³, Anatoly Gulyaev⁴, Maksim Moskovskiy⁴, Elena Zavyalova^2,4,a*

¹Northeast Normal University, Changchun, 130000, China

²Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia

³Department of Processes and Machines in Agribusiness, Kuban State Agrarian University named after I. T. Trubilin, 350044 Krasnodar, Russia

⁴Federal Scientific Agroengineering Center VIM, 109428 Moscow, Russia

^* To whom correspondence should be addressed.

Received: September 3, 2024; Revised: October 11, 2024; Accepted: October 21, 2024

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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.

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KEY WORDS: DNA, aptamer, biosensor, mycotoxin, DON, SERS

DOI: 10.1134/S000629792412006X

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