An In-Silico Pipeline for Rapid Screening of DNA Aptamers against Mycotoxins: The Case-Study of Fumonisin B1, Aflatoxin B1 and Ochratoxin A

Aptamers are single-stranded oligonucleotides selected by SELEX (Systematic Evolutionof Ligands by EXponential Enrichment) able to discriminate target molecules with high affinityand specificity, even in the case of very closely related structures. Aptamers have been producedfor several targets including small molecules like mycotoxins; however, the high affinity for theirrespective target molecules is a critical requirement. In the last decade, the screening throughcomputational methods of aptamers for their affinity against specific targets has greatly increased andis becoming a commonly used procedure due to its convenience and low costs. This paper describesan in-silico approach for rapid screening of ten ssDNA aptamer sequences against fumonisin B1(FB1, n = 3), aflatoxin B1 (AFB1, n = 2) and ochratoxin A (OTA, n = 5). Theoretical results werecompared with those obtained by testing the same aptamers by fluorescent microscale thermophoresisand by magnetic beads assay for their binding affinity (KD) revealing a good agreement.