Solid-Phase Collateral Cleavage System Based on CRISPR/Cas12 and Its Application toward Facile One-Pot Multiplex Double-Stranded DNA Detection

CRISPR/Cas Multiplexed Biosensing: Advances, Challenges, and Perspectives

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein systems are renowned for their high sensitivity and specificity, enabling them as a powerful diagnostic toolbox. Multiplexed detection of panels of targets, as opposed to single targets, is imperative for reliable and conclusive disease diagnostics. However, multiplex application of the CRISPR/Cas system has long been hindered by indistinguishable signals from specific targets due to nonspecific chaotic trans-cleavage. To make a breakthrough, substantial efforts have been devoted to CRISPR/Cas-powered multiplexed biosensing strategies, which consequently experienced rapid development over the past five years. This review systematically summarizes recent advances in CRISPR/Cas multiplexed detection encompassing Cas9, Cas12, and Cas13. Key focus issues include multiplex biosensing strategies and their respective advantages and limitations, sensing mechanisms, and detection performance of novel validated examples. Finally, the status and challenges of CRISPR/Cas multiplexed biosensing are critically discussed, and future outlooks are proposed for their potential practical application. This Perspective aims to inspire significant research and promote the development of the next generation of CRISPR/Cas multiplexed biosensing.

Dual-CRISPR/Cas12a-assisted RT-RAA visualization system for rapid on-site detection of nervous necrosis virus (NNV)

BACKGROUND

Nervous necrosis virus (NNV) poses a severe threat to the aquaculture industry, particularly infecting fish fry with devastating mortality rates and inflicting heavy economic losses. Traditional detection methods, such as cell culture and conventional RT-PCR, are not only time-consuming and require specialized laboratory facilities but also hard to eliminate contamination. Rapid and accurate on-site detection methods in aquaculture settings are crucial for effective control of NNV outbreaks in fish farms.

RESULTS

This study developed a one-tube visualization system for rapid and precise identification of NNV in a pond-side setting. This system utilizes the dual-clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a-assisted reverse transcription-recombinase aided amplification (RT-RAA) detection method, employing fluorescence intensity to indicate positive results for easy interpretation by field operators. The key to this system involved the meticulous selection of RT-RAA primer sets and CRISPR RNA (crRNA) primer sets targeting two genes of NNV, the capsid protein (CP) and RNA-dependent RNA polymerase (RdRp), distributing on two particles of genomic sequences. The assay demonstrated a speed and efficiency process within 30 min and a detection limit of 0.5 copies/μL, achieving 100 % accuracy when compared to qRT-PCR. The practical utility and effectiveness were validated by using 32 field samples. The results underscored the simplicity, rapidity, and reliability of the system, confirming its potential as a robust tool for NNV diagnosis in fish farms.

SIGNIFICANCE

This study introduces the first application of a dual-CRISPR/Cas12a-assisted RT-RAA visualization system for diagnosing NNV infections. The novel approach substantially enhances on-site diagnostic capabilities, offering a rapid, reliable, and cost-effective solution for fish farm operators. This innovation not only streamlines the detection process but also ensures timely intervention, thereby mitigating the impact of NNV on aquaculture.

Miniaturization of CRISPR/Cas12-Based DNA Sensor Array by Non-Contact Printing

DNA microarrays have been applied for comprehensive genotyping, but remain a drawback in complicated operations. As a solution, we previously reported the solid-phase collateral cleavage (SPCC) system based on the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 12 (CRISPR/Cas12). Surface-immobilized Cas12-CRISPR RNA (crRNA) can directly hybridize target double-stranded DNA (dsDNA) and subsequently produce a signal via the cleavage of single-stranded DNA (ssDNA) reporter immobilized on the same spot. Therefore, SPCC-based multiplex dsDNA detection can be performed easily. This study reports the miniaturization of SPCC-based spots patterned by a non-contact printer and its performance in comprehensive genotyping on a massively accumulated array. Initially, printing, immobilization, and washing processes of Cas12-crRNA were established to fabricate the non-contact-patterned SPCC-based sensor array. A target dsDNA concentration response was obtained based on the developed sensor array, even with a spot diameter of 0.64 ± 0.05 mm. Also, the limit of detection was 572 pM, 531 pM, and 3.04 nM with 40, 20, and 10 nL-printing of Cas12-crRNA, respectively. Furthermore, the sensor array specifically detected three dsDNA sequences in one-pot multiplexing; therefore, the feasibility of comprehensive genotyping was confirmed. These results demonstrate that our technology can be miniaturized as a CRISPR/Cas12-based microarray by using non-contact printing. In the future, the non-contact-patterned SPCC-based sensor array can be applied as an alternative tool to DNA microarrays.