CRISPR/Cas13 system-based entropy-driven DNAzyme switch powered DNA walking system for sensitive and direct rotavirus detection

Abstract

DNA walker–based strategies are confronted with significant challenges in harmonizing design complexity, sequence dependence, and amplification efficiency. This study describes the innovative design of a double-stranded DNA probe, named the “LW probe,” which integrates a locked DNAzyme segment, enabling the coupling of the entropy-driven amplification (EDA) process with a DNAzyme-powered DNA walker. In the absence of the target, the “LW probe” remains in an inactive (“OFF”) state. Upon encountering target rotavirus sequences, the LW probe receives the trans-cleavage activity of Cas13a/crRNA and undergoes a conformational change, transforming into an activated structure. This structural transition initiates the EDA process continuously, leading to the release of the DNAzyme segment. Subsequently, the released DNAzyme segment acts on the surface of gold nanoparticles (AuNPs), cleaving the “Substrate probe” and consequently liberating fluorescence signals. Distinct from traditional DNA walkers that rely exclusively on the EDA for product amplification, the proposed approach synergistically combines the high-precision target recognition capacity of the EDA process with the potent signal amplification efficiency of DNA walkers. This integration results in remarkable enhancements in both specificity, demonstrated by the ability to discriminate single-base mismatched sequences, and sensitivity, with a detection limit as low as 2.7 fM. By synergizing EDA with the DNAzyme-driven DNA walker, our method achieves high sensitivity, with a detection limit of 2.7 fM, outperforming or matching the performance of previous DNA walker-based systems. This system enables highly sensitive and specific detection of low-abundance rotavirus with robust stability, offering a promising platform for disease diagnosis and biomedical research.

Graphical abstract