Introducing truncated DNA aptamer as a new molecular probe for aflatoxin B1 detection using computational simulation techniques

Single strand DNA or RNA known as aptamers, are able to detect the target molecule with specificity at the monoclonal antibody level. However, the placement of mycotoxins in small molecule groups and their high molecular weight differences with aptamers have become a serious challenge in introducing aptameric probes for them. In the present study, in order to achieve a new and shorter aptamers sequence for aflatoxin B1 (AFB1), an initial oligonucleotide library (Lib1) was designed based on the sequence of a known AFB1 aptamer (named Apt1, 50 bp) using the genetic algorithm. The best aptamer from the Lib1 library was selected based on the molecular docking results and has been modified to create a new library (Lib2) using the truncating strategy. Virtual screening of the Lib2 library in terms of their binding affinity over AFB1 molecule led to obtain the truncated aptamer, C52-T, with 19 bp in length. Type of interaction and stability of C52-T-AFB1 complex were investigated using molecular dynamics simulations (MD) and MM-PBSA method. The affinity constant of C52, C52-T and Apt1 aptamers over AFB1 were estimated through unmodified gold nanoparticle-based colorimetric assay. The experimentally founding and in silico results were completely consistent. It seems that the computational techniques have the great potential to introduce sensitive molecular probes to design specific mycotoxins aptasensors.