Structural insights into the AFB1 aptamer coupled with a rationally designed CRISPR/Cas12a-Exo III aptasensor for AFB1 detection

Pengfei Ma; Hualin Guo; Hua Ye; Yin Zhang; Zhouping Wang

doi:10.1016/j.ijbiomac.2022.11.177

Structural insights into the AFB₁ aptamer coupled with a rationally designed CRISPR/Cas12a-Exo III aptasensor for AFB₁ detection

Int J Biol Macromol. 2023 Jan 15:225:1164-1171. doi: 10.1016/j.ijbiomac.2022.11.177. Epub 2022 Nov 19.

Authors

Pengfei Ma¹, Hualin Guo¹, Hua Ye², Yin Zhang³, Zhouping Wang⁴

Affiliations

¹ State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China.
² School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China.
³ Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China.
⁴ State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China; School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212004, China. Electronic address: wangzp@jiangnan.edu.cn.

PMID: 36414074
DOI: 10.1016/j.ijbiomac.2022.11.177

Abstract

Aflatoxin B₁ (AFB₁) is a typical food contaminant. A truncated DNA aptamer of AFB₁ was reported by our team in previous work. However, the recognition mechanism between aptamer and AFB₁ was lacking, which was crucial for the design of related aptasensor. Herein, the binding of aptamer to AFB₁ was systematically studied and found that it was an exothermic process and the conformation of aptamer changed during the recognition process. Loop bases in the secondary structure of aptamer formed a special binding pocket to recognize AFB₁. Van der Waals and electrostatic interaction were the main driving forces. By blocking the stem bases guided by the structural investigation, a rationally designed CRISPR/Cas12a-Exo III aptasensor for AFB₁ detection was constructed, and the sensitivity was improved by target recycling. Under optimal conditions, the linear detection range for AFB₁ was 0.01-20 ng/mL, and AFB₁ was accurately determined in corn and wheat samples. This work laid a theoretical foundation for the design of AFB₁ aptasensor, and the developed detection model came up with new ideas for the development of CRISPR/Cas12a-based aptasensor.

Keywords: AFB(1) aptamer; Binding mechanism; CRISPR/Cas12a-Exo III.

MeSH terms

Aflatoxin B1 / chemistry
Aptamers, Nucleotide* / chemistry
Biosensing Techniques*
CRISPR-Cas Systems / genetics
Food Contamination / analysis
Limit of Detection

Substances

Aptamers, Nucleotide
Aflatoxin B1