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

Maryam Mousivand; Laura Anfossi; Kowsar Bagherzadeh; Nadia Barbero; Amir Mirzadi-Gohari; Mohammad Javan-Nikkhah

doi:10.1016/j.aca.2020.01.045

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

Anal Chim Acta. 2020 Apr 8:1105:178-186. doi: 10.1016/j.aca.2020.01.045. Epub 2020 Jan 24.

Authors

Maryam Mousivand¹, Laura Anfossi², Kowsar Bagherzadeh³, Nadia Barbero⁴, Amir Mirzadi-Gohari⁵, Mohammad Javan-Nikkhah⁶

Affiliations

¹ Department of Plant Protection, College of Agricultural Sciences & Engineering, University of Tehran, Karaj, 31587-77871, Iran; Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, 3135933151, Karaj, Iran.
² Department of Chemistry and NIS Interdepartmental Center, University of Turin, Via Pietro Giuria 5, 7, 10125, Turin, Italy; Department of Chemistry, University of Turin, Via Giuria, 5, I-10125, Turin, Italy. Electronic address: laura.anfossi@unito.it.
³ Eye Research Center, The Five Senses Institute Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran; Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran.
⁴ Department of Chemistry and NIS Interdepartmental Center, University of Turin, Via Pietro Giuria 5, 7, 10125, Turin, Italy; Department of Chemistry, University of Turin, Via Giuria, 5, I-10125, Turin, Italy.
⁵ Department of Plant Protection, College of Agricultural Sciences & Engineering, University of Tehran, Karaj, 31587-77871, Iran.
⁶ Department of Plant Protection, College of Agricultural Sciences & Engineering, University of Tehran, Karaj, 31587-77871, Iran. Electronic address: jnikkhah@ut.ac.ir.

PMID: 32138917
DOI: 10.1016/j.aca.2020.01.045

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 AFB_1. The ISM allowed the identification of an aptamer, F20, with up to 9.4 and 2 fold improvement in affinity and selectivity compared to the parent aptamer, respectively.

Keywords: Aflatoxin B(1); Aptamer; Fluorescent anisotropy; Genetic algorithm; Gold nanoparticles; Molecular docking.

MeSH terms

Aflatoxin B1 / analysis*
Aptamers, Nucleotide / chemistry*
Biosensing Techniques*
Gold / chemistry
Metal Nanoparticles / chemistry
Molecular Docking Simulation

Substances

Aptamers, Nucleotide
Gold
Aflatoxin B1