The design strategies for CRISPR-based biosensing: Target recognition, signal conversion, and signal amplification

High-fidelity telomerase activity assay based on light-triggered nucleic acid separation system for the diagnosis of bladder cancer

In conventional methods for telomerase activity assay, the obtained telomerase sample contains a large amount of impurity, which seriously affect the accuracy of the assay. Herein, we propose a light-triggered nucleic acid separation strategy to realize high fidelity Telomerase activity assay (Lit-Telo). In the light-triggered nucleic acid separation system, a 5' terminal biotinylated and photo-cleavable (PC) linker-functionalized telomerase substrate probe (Bio-PCTS) is designed. Telomerase extends telomeric repeat DNA (TTAGGG) to the 3' terminal of Bio-PCTS probe to produce telomerase extension product, which can be captured by streptavidin coated 96-well plate. Thus, the impurity can be removed from the reaction to realize the purification of telomerase extension product. A few seconds of UV light irradiation can disrupt the PC-linker in Bio-PCTS probe, allowing the easy and quick release of the telomerase extension product DNA fragment from the bottom of 96-well plate into the reaction solution for subsequent detection. Asymmetric-PCR-based TRAP and LbaCas12a/crRNA system were elucidated and optimized to realize the enhanced detection of telomerase activity. The proposed Lit-Telo platform achieved a limit-of-detection of telomerase activity equivalent to 8 HeLa cells. 26 bladder specimens were collected for telomerase activity assay using both fluorescence detection based Lit-Telo (Fluo Lit-Telo) visual detection based Lit-Telo (Visual Lit-Telo). ROC (receiver operating characteristic curve) analysis of the data indicated the good detection accuracy of Fluo Lit-Telo and Visual Lit-Telo methods with the AUC value of 93.94% and 92.12%, respectively. These results demonstrated the potential of the Lit-Telo platform in the in vitro diagnosis of bladder cancer.

CRISPR-Based Regulation for High-Throughput Screening

CRISPR technology has revolutionized genome editing by enabling precise, permanent modifications to genetic material. To circumvent the irreversible alterations associated with traditional CRISPR methods and facilitate research on both essential and nonessential genes, CRISPR interference or inhibition (CRISPRi) and CRISPR activation (CRISPRa) were developed. The gene-silencing approach leverages an inactivated Cas effector protein paired with guide RNA to obstruct transcription initiation or elongation, while the gene-activation approach exploits the programmability of CRISPR to activate gene expression. Recent advances in CRISPRi technology, in combination with other technologies (e.g., biosensing, sequencing), have significantly expanded its applications, allowing for genome-wide high-throughput screening (HTS) to identify genetic determinants of phenotypes. These screening strategies have been applied in biomedicine, industry, and basic research. This review explores the CRISPR regulation mechanisms, offers an overview of the workflow for genome-wide CRISPR-based regulation for screens, and highlights its superior suitability for HTS across biomedical and industrial applications. Finally, we discuss the limitations of current CRISPRi/a HTS screening methods and envision future directions in CRISPR-mediated HTS research, considering its potential for broader application across diverse fields.

Catalytic hairpin assembly-coupled CRISPR/Cas12a biosensor for sensitive detection of melamine in dairy products

We combined catalytic hairpin assembly (CHA) with the Cas12a system for detecting melamine adulteration. This system involved two-step signal conversion and two-level amplification, boosting the sensor's versatility and sensitivity. The sensor showed excellent specificity and applicability for melamine detection in dairy products, and was broadened to viral nucleic acid detection.

Polydopamine Powered Droplet Electricity Generator for Protein Assay with CRISPR/Cas Enabled Amplification

Protein function investigation and clinical assay are fundamental to modern biology and medical diagnostics. Flap endonuclease 1 (FEN1), a key enzyme in DNA replication and repair, plays a critical role in the progression of many diseases. Taking FEN1 as an example, we present a novel protein detection platform combining triboelectric nanogenerator (TENG) and CRISPR/Cas technologies. As a specific form of TENG, the transistor-droplet electricity generator (TDEG) is explored, which offers a low-cost, simple fabrication approach with real-time detection capability. Meanwhile, the FEN1 activated CRISPR/Cas system catalyzes the reactions on the three-dimensional DNA tetrahedron interface, promising the high sensitivity. This work not only demonstrates a powerful method for rapid protein detection but also pioneers the integration of CRISPR/Cas with TENG. It has a great prospect for future development of TENG sensors.

CRISPR/HCR-powered ratiometric fluorescence aptasensor for ochratoxin A detection

To address the need for highly sensitive and reliable detection of trace ochratoxin A (OTA) in food matrices, we developed a ratiometric fluorescent aptasensor by integrating CRISPR/Cas12a, hybridization chain reaction (HCR), and horseradish peroxidase (HRP)-induced inner filter effect (IFE). The mechanism involves OTA releasing an activator that initiates CRISPR/Cas12a trans-cleavage, blocking HCR assembly. This reduces HRP levels, limiting the conversion of o-phenylenediamine (OPD) to fluorescent 2,3-diaminophenazine (DAP) (emitting at 562 nm) while maintaining strong emission from 2-amino terephthalic acid (BDC-NH2) at 426 nm. The F426/F562 ratio serves as a "signal-on" indicator, enabling sensitive OTA detection over 0.1 pM to 10 nM, with a detection limit of 0.0417 pM. The method exhibits excellent reproducibility, with intra-day and inter-day relative standard deviations (RSDs) of 1.91 %-3.87 % and 1.79 %, respectively, along with recovery rates of 90.1 %-110.6 % in real samples. These advantages highlight its significant potential for CRISPR/Cas-based OTA detection.

Recent Advances in Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Proteins System-Based Biosensors

High-sensitivity and high-specificity biodetection is critical for advancing applications in life sciences, biosafety, food safety, and environmental monitoring. CRISPR/Cas systems have emerged as transformative tools in biosensing due to their unparalleled specificity, programmability, and unique enzymatic activities. They exhibit two key cleavage behaviors: precise ON-target cleavage guided by specific protospacers, which ensures accurate target recognition, and bystander cleavage activity triggered upon target binding, which enables robust signal amplification. These properties make CRISPR/Cas systems highly versatile for designing biosensors for ultra-sensitive detection. This review comprehensively explores recent advancements in CRISPR/Cas system-based biosensors, highlighting their impact on improving biosensing performance. We discuss the integration of CRISPR/Cas systems with diverse signal readout mechanisms, including electrochemical, fluorescent, colorimetric, surface-enhanced Raman scattering (SERS), and so on. Additionally, we examine the development of integrated biosensing systems, such as microfluidic devices and portable biosensors, which leverage CRISPR/Cas technology for point-of-care testing (POCT) and high-throughput analysis. Furthermore, we identify unresolved challenges, aiming to inspire innovative solutions and accelerate the translation of these technologies into practical applications for diagnostics, food, and environment safety.

A CRISPR/Cas12a-based competitive aptasensor for ochratoxin A detection

The serious contamination of ochratoxin A (OTA) in agricultural products has promoted the development of rapid, sensitive, and selective analytical methods for OTA monitoring. We demonstrated a competitive aptasensor for OTA detection using CRISPR/Cas12a as an effective signal amplifier. OTA competes with complementary DNA of the aptamer on the microplate to bind to the aptamer. Streptavidin bridges the biotinylated aptamer and biotinylated activator to convert the OTA input into Cas12a activation, which cleaves fluorescent DNA reporters. Under optimized experimental conditions, the aptasensor was demonstrated to work well for sensitive detection of OTA, with a linear range from 0.5 nM to 62.5 nM and a detection limit of 0.5 nM. Moreover, our method not only exhibits high selectivity, but also has satisfactory anti-interference ability against complex sample matrices. Taken together, the CRISPR/Cas12a-based competitive aptasensor offers a simple and sensitive platform for OTA detection, and it holds great promise for food security monitoring.

Rapid and accurate SERS assay of disease-related nucleic acids based on isothermal cascade signal amplifications of CRISPR/Cas13a system and catalytic hairpin assembly

Developing rapid, accurate and convenient nucleic acid diagnostic techniques is essential for the prevention and control of contagious diseases that are prone to gene mutations and may have homologous sequences, especially emerging infectious diseases such as the SARS-CoV-2 pandemic. Herein, a one-pot SERS assay integrating isothermal cascade signal amplification strategy (i.e., CRISPR/Cas13a system (Cas13a) and catalytic hairpin assembly (CHA), Cas13a-CHA) and SERS-active silver nanorods (AgNRs) sensing chips was proposed for rapid and accurate detection of disease-related nucleic acids. Taking SARS-CoV-2 RNA assay as a model, the Cas13a-CHA based SERS sensing strategy can achieve ultra-high sensitivity low to 5.18 × 102 copies·mL-1 within 60 min, and excellent specificity, i.e., not only the ability to identify SARS-CoV-2 RNA from gene mutations, but also incompatibility with coronaviruses such as severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV), and other respiratory viruses. The proposed Cas13a-CHA based SERS assay for SARS-CoV-2 RNA has satisfactory sensitivity, specificity, uniformity, and repeatability, and can be easily expanded and universalized for screening different viruses, which is expected to promise as a crucial role for diagnosis of disease-related nucleic acids in various medical application scenarios.