In silico maturation of affinity and selectivity of DNA aptamers against aflatoxin B1 for biosensor development

Analytica Chimica Acta
Maryam MousivandMohammad Javan-Nikkhah

Abstract

A high affinity and selectivity DNA aptamer for aflatoxin B1 (AFB1) was designed through Genetic Algorithm (GA) based in silico maturation (ISM) strategy. The sequence of a known AFB1 aptamer (Patent: PCT/CA2010/001292, Apt1) applied as a probe in many aptasensors was modified using seven GA rounds to generate an initial library and three different generations of ss DNA oligonucleotides as new candidate aptamers. Molecular docking methodology was used to screen and analyze the best aptamer-AFB1 complexes. Also, a new pipeline was proposed to faithfully predict the tertiary structure of all single stranded DNA sequences. By the second generation, aptamer Apt1 sequence was optimized in the local search space and five aptamers including F20, g12, C52, C32 and H1 were identified as the best aptamers for AFB1. The selected aptamers were applied as probes in an unmodified gold nanoparticles-based aptasensor to evaluate their binding affinity to AFB1 and their selectivity against other mycotoxins (aflatoxins B2, G1, G2, M1, ochratoxin A and zearalenone). In addition, a novel direct fluorescent anisotropy aptamer assay was developed to confirm the binding interaction of the selected aptamers over AFB1. The ISM allowed the identificatio...Continue Reading

Citations

Jan 14, 2021·Analytical Methods : Advancing Methods and Applications·Chengquan WangXingyi Huang
Mar 7, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Zidane QriouetZineb Qmichou
Mar 26, 2021·Journal of Molecular Graphics & Modelling·Nor Azlina AhmadMuhammad Helmi Nadri
Jun 8, 2021·Nucleic Acids Research·Kaori TsukakoshiKazunori Ikebukuro

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