CRISPR/Cas12a triggered SERS and naked eye dual-mode biosensor for ultrasensitive and on-site detection of nucleic acid via cascade signal amplification

Highly sensitive and on-site detection of nucleic acids has always been a critical issue in the field of analytical chemistry. Surface-enhanced Raman scattering (SERS)-based biosensing exhibits huge potential in nucleic acid detection, while the applicability is restricted in trace nucleic acid screening due to the lack of appropriate signal recognition, transducing and amplification technologies. Inspired by the specific recognition of CRISPR/Cas12a and the improved sensitivity through cascade signal amplification, we innovatively proposed a CRISPR/Cas12a triggered SERS and naked eye dual-mode biosensor for ultrasensitive and on-site detection of nucleic acid via cascade signal amplification. Upon the target DNA recognition, the activated CRISPR/Cas12a indiscriminately cleaved substrate ssDNA, leading to the failure of toehold-mediated DNA-strand displacement reaction (TSDR), and triggering hybridization chain reaction (HCR) to assemble numerous G-quadruplex/hemin DNAzyme (GQH DNAzyme) for cascade signal amplification. The generated GQH DNAzyme catalyzed the oxidation of l-cysteine to cystine, perturbing the aggregation of 4-NTP@AuNPs, resulting in significant Raman signal change. On the other hand, GQH DNAzyme catalyzed the oxidation of 2,2′-azino-di-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS), leading to obvious color change to realize portable naked-eye detection. Through this strategy, target nucleic acid concentration was tactfully transformed into sensitive Raman and portable visualization signals, and the limit of detection were as low as 34.9 aM and 1 pM, respectively. Then, this biosensor was successfully applied to meat adulteration detection, which showed superb selectivity, sensitivity and applicability for on-site detection of trace nucleic acid in complicated food matrix.