Computer aided aptamer selection for fabrication of electrochemical sensor to detect Aflatoxin B₁

Abstract

Aflatoxin B₁ (AFB₁) is a naturally occurring toxin produced by Aspergillus flavus and Aspergillus parasiticus. The AFB₁ is classified as a potent carcinogen and poses significant health risks both to humans and animals. Early detection of the toxin in post-harvest agricultural products will save lives and promote healthy food production. In this study, stratified docking approach was utilized to screen and identify potential aptamers that can bind to AFB₁. ssDNA sequences were acquired from the Mendeley dataset, secondary and tertiary structures were predicted through a series of bioinformatics pipelines. Further, the final DNA tertiary structures were minimized and SiteMap algorithm was used to probe and locate binding cavities. According to the final XP docking result, a 34 nt sequence (5′-ATCCTGTGAGGAATGCTCATGCATAGCAAGGGCT-3′) aptamer with a docking score of −5.959 kcal/mol was considered for 200 ns MD Simulation. Finally, the screened DNA-aptamer was immobilized over the gold surface based on Au-S chemistry and utilized for the detection of AFB₁. The fabricated DNA-aptamer electrode demonstrated a good analytical performance including wide linear range (1.0 to 1000 ng L⁻¹), detection limit (1.0 ng L⁻¹), high stability, and reproducibility.

Communicated by Ramaswamy H. Sarma

Keywords:

• Aflatoxin B₁ detection
• in silico-based aptamer maturation
• XP docking
• electrochemical detection

Author contribution

Misgana Mengistu Asmare: Conceptualization, Methodology, Literature Review, Investigation, Formal analysis, Writing—original draft, Writing-review & editing. Chandran Krishnaraj: Conceptualization, Literature Review, Methodology, Investigation, Formal analysis, Writing—review & editing. Sivaprakasam Radhakrishnan: Methodology, Writing—review & editing of biosensor part. Byoung-Suhk Kim: Writing—review & editing, Supervision. Soon-Il Yun: Writing—review & editing, Supervision, Project administration, Funding acquisition.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This project was supported by the Basic Science Research Program through National Research Foundation of Korea, NRF-2021R1A2C1094316.