Chemical additives-enhanced CRISPR/Cas12a-based RNA detection.

TOPS-CRISPR: Thermally-regulated and oligonucleotide-mediated one-pot CRISPR-Cas12a assay for ultra-sensitive and rapid on-site diagnostics.

CRISPR-Cas12a has emerged as a powerful tool in molecular diagnostics, owing to its robust signal amplification and compact crRNA design. However, its uncontrolled enzymatic activity often hampers application in streamlined one-pot assays. Although existing temporal or spatial regulation strategies can mitigate this issue, they typically introduce operational complexity or increased cost. Here, we designed a Thermally regulated, Oligonucleotide-mediated one-Pot System for CRISPR-Cas12a (TOPS-CRISPR), which employs a programmable inhibition strategy based on complementary RNA blockers with tunable length and binding sites, enabling efficient and reversible steric inhibition of the LbCas12a-crRNA ribonucleoprotein (RNP) complex, resolving the inherent contradiction between amplification and cleavage in one-pot assay. TOPS-CRISPR not only is operational simple and cost-effective but also achieves over 60-fold higher sensitivity than conventional one-pot platforms. We demonstrated the clinical applicability of TOPS-CRISPR by accurately detecting Brucella and Streptococcus in both spiked and clinical samples. Moreover, the system integrates seamlessly with rapid sample processing, lyophilized reagents, and miniaturized workflows, enabling field-deployable pathogen identification within 50 min.

Strategic Design and Engineering of CRISPR/Cas-Powered Sensing Platforms for Enhanced Nucleic Acid Detection.

Rapid and accurate nucleic acid detection is fundamental to effective disease management. While PCR remains the gold standard, its requirement for sophisticated instrumentation limits its application in point-of-care settings. CRISPR-Cas systems have emerged as a disruptive diagnostic technology, leveraging the programmable specificity and unique trans-cleavage activity of Cas effectors to revolutionize biosensing. This review systematically evaluates the evolution of CRISPR-Cas-powered sensing platforms, categorized by their signal transduction modalities. We first discuss the expanding biochemical landscape of Cas nucleases, highlighting recent discoveries where conventional boundaries of Cas9, Cas12, and Cas13 have been transcended to enable versatile DNA/RNA targeting. Subsequently, we provide a comprehensive analysis of four primary sensing architectures: (1) Fluorescence-based platforms, exploring diverse strategies from target and signal amplification with dual-labeled ssDNA probes to nanomaterial-based probes; (2) Naked-eye visual platforms, encompassing both solid-phase lateral flow assays and solution-phase colorimetric strategies that facilitate rapid, instrument-free screening; (3) Electrochemical biosensors, which transduce biological recognition events into measurable electrical parameters, offering high sensitivity and seamless integration with miniaturized electronics; and (4) Electronic and Optoelectronic systems, including field-effect transistors and plasmonic sensors, which offer high-sensitivity, label-free detection. Despite significant progress, the translation of CRISPR-Dx from laboratory proof of concepts to clinical reality faces several bottlenecks. We critically analyze current challenges, including the need for integrated "sample-to-answer" workflows, high-throughput multiplexing, and digital quantification. Finally, we envision future trends such as AI-assisted signal processing and wearable sensing interfaces. By bridging the gap between molecular biology and advanced engineering, CRISPR-powered platforms are poised to make precision molecular diagnostics universally accessible.

A One-Pot Reverse Transcriptase-Mediated, Pre-amplification-Free CRISPR/Cas12a Assay for Ultrasensitive Nucleic Acid Detection.

CRISPR/Cas12a holds great promise for biosensing and diagnostics, but conventional methods suffer from low catalytic efficiency, high background, and reliance on pre-amplification. Direct detection of structured RNAs also remains challenging. Herein, we report the development of a reverse transcriptase and LNA probe (LNA-p)-mediated CRISPR/Cas12a positive feedback system (RTLC) for highly efficient, one-pot detection of both DNA and RNA. Without pre-amplification or thermal cycling, the assay achieves a 0.5 aM detection sensitivity within 27 min, exhibits single-base resolution, and allows direct detection of RNAs up to 985 nt in length. Together, RTLC is successfully validated in practical samples by detecting lncRNA HULC and miR-21, offering a robust, versatile tool for high-performance nucleic acid diagnostics.

Programmable Allosteric DNAzyme Coupled with CRISPR/Cas12a System for Multiplexed and Sensitive Detection of Extracellular Vesicle Derived MicroRNAs

Isothermal miRNA Detection via Ligation-Dependent CRISPR/Cas13a Activation

Here, we present a rapid isothermal strategy for miRNA detection based on ligation-dependent generation of Cas13a-activating RNA and CRISPR/Cas13a-mediated signal amplification. The system employs two DNA probes: a hairpin-structured probe containing a double-stranded T7 promoter within its stem and a second probe encoding a template for Cas13a activator RNA. In the presence of a target miRNA, the probes are ligated to form a functional transcription template, enabling the generation of Cas13a-activating RNA. The resulting RNA activates the Cas13a–crRNA complex, inducing collateral cleavage of a fluorescent reporter for signal generation. The method achieves a limit of detection of 2.56 pM for miR-21 and 11.64 pM for miR-10a, with a linear response over 0–500 pM, while maintaining high specificity with negligible responses to nontarget miRNAs. Importantly, the entire assay is completed within 40 min at 37 °C, highlighting its rapid detection capability. The applicability of the platform is validated using miRNA extracted from HepG2, HeLa, and MCF-7 cells, yielding results consistent with RT-qPCR analysis. Owing to its short assay time, operation at 37 °C, and sequence programmability through probe redesign, this strategy provides a useful framework for miRNA detection.

Bead-based RNA Detection with Cas13a: Multi-scale Design and Validation

CRISPR-based assays offer sensitive and specific nucleic acid detection for a broad range of diagnostic and surveillance applications. While standard solution-based assays are simple, they typically lack the ability to detect multiple targets individually without the need for more complex instrumentation and multi-step workflows. Surface-based strategies offer greater potential for multiplexing since the identity of a target can be associated with a location on a slide or a specific bead, as in the case of DNA arrays or Luminex bead assays. However, the design principles for optimizing surface-based CRISPR assays have yet to be developed. Here we present a multi-scale analytical framework integrating nanoscale enzyme kinetics, microscale diffusion constraints, and macroscale assay parameters that we use to develop a bead-based Cas13a assay where the bead becomes fluorescent when the target RNA for that bead is detected. The assay, which we call SurfCas, uses surface-bound guide RNAs and reporter RNAs to detect one or more soluble target RNAs in a one-pot assay. We show that SurfCas has a sensitivity approaching bulk reactions, and we demonstrate multiplexed detection of target RNAs in a complex biological matrix. The design principles we establish for surface-based CRISPR assays offer guidance on how to further improve SurfCas sensitivity and scale multiplexed detection of target RNAs in a single reaction.