Dual DNA recycling amplification-assisted CRISPR/Cas12a cleavage for dual-channel ratiometric fluorescence biosensing of kanamycin antibiotic

Abstract

Fluorescence biosensors hold significant importance for testing antibiotic residues which seriously endanger public health. However, how to adopt appropriate strategies to address the false result disadvantage involved in traditional single-channel biosensors is still a great challenge. Meanwhile, too much attention focused on designing signal amplification strategies of biosensors unavoidably decreases their detection efficiency. Herein, we combined the designed dual DNA recycling amplification strategy with CRISPR/Cas12a-mediated dual-channel signal output mode to successfully develop a novel ratiometric fluorescence biosensor for testing kanamycin (Kana) residues in complex sample matrices. The first recycling was formed from an exonuclease-assisted aptamer recognition reaction, which also triggered another cascade DNA recycling to amplify the release of the Cas12a activator. With the non-discrimination cleavage of Cas12a to cause reverse fluorescence changes of copper nanoclusters and an AMAC-labeled signal DNA, the ratiometric signal transduction strategy was constructed. Under optimal conditions, this biosensor could be applied for ultrasensitive testing of Kana antibiotics in a five-order of magnitude wide linear range with a low detection limit of 17.2 fg mL^-1. Benefiting from the self-correction function of the ratiometric signal transduction mode, it showed promising practicality in lake water and milk samples with the relative error less than 4.9% to the standard ELISA results. Besides CRISPR/Cas12a-based fluorescence output efficiency improvement, this biosensor also excluded the complicated manipulations and expensive instruments required in traditional methods. Therefore, it provides a good choice for expanding the application of fluorescence biosensing technology for practical analysis application.

Keywords: Antibiotic testing; CRISPR/Cas12a; Fluorescence biosensors; Functional nucleic acid; Ratiometric analysis.