A Simple Programmable Cas12a/crRNA Induced Walking System for Sensitive Methicillin-Resistant Staphylococcus aureus Detection via Integrated cis- and trans-Cleavage Activity

TL;DR

This paper introduces a new CRISPR-based method for detecting MRSA bacteria with high sensitivity and specificity using a programmable Cas12a system.

Contribution

A novel programmable Cas12a system using a structure-switchable probe that integrates cis- and trans-cleavage activities for MRSA detection.

Findings

The method achieved a detection limit of 2.5 CFU/ml for MRSA with high specificity.

The design simplifies probe architecture while maintaining efficient signal amplification.

The system uses a hairpin-structured locker-probe to regulate Cas12a trans-cleavage activity.

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) represents a serious threat to public health due to its strong antibiotic resistance, wide dissemination, and high infection rates. Rapid identification of MRSA strains is essential for accurate diagnosis and timely treatment of related infections. In this study, we propose an analytical method for MRSA that employs a hairpin-structured locker-probe to directly regulate the trans-cleavage activity of Cas12a. This designed locker-probe connects a target-specific aptamer to an inhibitory aptamer of the CRISPR/Cas12a system. Upon binding to the specific target, the probe undergoes a conformational change that abolishes its inhibitory effect on Cas12a. As a result, the structure-switchable probe modulates Cas12a activity in a target-dependent manner. Additionally, the sensing substrate combines a “cis-cleavage trigger” and a “trans-cleavage trigger” to integrate both cis- and trans-cleavage activities of Cas12a/crRNA within a single probe. This design significantly simplifies the probe architecture while maintaining high signal amplification efficiency. The proposed method was successfully applied to detect MRSA, achieving a detection limit as low as 2.5 CFU/ml with high specificity. By exploiting the inhibitory aptamer of Cas12a as a regulatory element for MRSA analysis, this work expands the toolbox of CRISPR/Cas12a-based methodologies and offers a promising strategy for bacterial detection.

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