CRISPR/Cas12a-Responsive Hydrogels for Conjugation-Free and Universal Indicator Release in Colorimetric Detection

ID-CRISPR: A CRISPR/Cas12a platform for label-free and sensitive detection of rare mutant alleles using self-interference DNA hydrogel reporter

Accurate and sensitive detection of single nucleotide variants (SNVs) is paramount for cancer diagnosis and treatment. The CRISPR/Cas12a system shows promise for SNV detection due to its high sensitivity and single-base specificity. However, most CRISPR/Cas12a-based methods rely on F/Q-labeled single-stranded DNA (ssDNA) reporters, which are susceptible to fluorescence fluctuations, thereby reducing accuracy. To address these limitations, researchers have proposed using DNA hydrogels as signal transducers in CRISPR/Cas12a systems. Yet, the encapsulation of indicators into DNA hydrogels introduces additional instability, which could compromise both detection sensitivity and linearity. In this study, we integrated hyperspectral interferometry into a DNA hydrogel-based CRISPR/Cas12a detection platform (ID-CRISPR) to achieve sensitive label-free SNV detection. Using EGFR L858R SNV as a model target, we demonstrated that ID-CRISPR can detect mutant allele frequencies (MAFs) as low as 0.1% with a limit of detection (LOD) of 5 aM, while also showing its potential for quantifying SNV abundance. Its clinical utility was confirmed through analysis of lung tumor samples, with results consistent with sequencing data. Therefore, ID-CRISPR provides a sensitive, label-free, and user-friendly platform for SNV detection, offering new insights into combining optical sensing with DNA hydrogel technology in CRISPR/Cas assays.

BE-CATCH: Bioamplifier-Equipped CRISPR-Cas12a Transduction System Coupled with Commercial Pregnancy Test Strips to Harness Signal-on Point-of-Care Detection

Repurposing existing commercial diagnostic equipment to enable portable analysis of diverse targets is driving the development of affordable point-of-care testing (POCT). Interestingly, we found that goat antimouse IgG could replace human chorionic gonadotropin (hCG) to make the T line of pregnancy test strips (PTS) appear red color and accordingly synthesized a novel signal output probe, which eliminated the intricate hCG covalent coupling steps, and could meet the multiple needs of expanded POCT. Given this, we introduced a novel separation-free universal POCT strategy termed bioamplifier-equipped CRISPR-Cas12a transduction system coupled with PTS to harness signal-on detection (BE-CATCH). Specifically, target inputs were converted and amplified by the multiplied strand displacement amplification-based bioamplifier, thereby activating Cas12a's trans-cleavage activity. Then, the activated Cas12a would cleave the connector indiscriminately, which ultimately kept the signal output probe in a free state; thus, the inputs could be translated into a colorimetric signal on the PTS. This strategy not only provided boosted sensitivity and specificity but also enhanced user-friendliness by maintaining the signal-on detection mode. We also demonstrated the versatility of the BE-CATCH strategy through selectively detecting miR-155 and flap endonuclease 1. Given its broad adaptability, the BE-CATCH strategy could provide an appealing option to broaden the application of PTS in biomedical diagnostics.

Fast-Flu: RT-RPA-CRISPR/Cas12a assisted one-step platform for rapid influenza B virus detection

Influenza B virus (Flu B) is a prevalent respiratory pathogen responsible for seasonal influenza epidemics. Despite its clinical significance, there remains a lack of rapid and accurate diagnostic methods for Flu B detection. In this study, we developed a novel Flu B detection system, named Fast-Flu, by integrating reverse transcription recombinase polymerase amplification (RT-RPA) with the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system (CRISPR/Cas). Through optimization of reaction temperature and adjustment of Cas12a concentrations, we successfully balanced RPA amplification and CRISPR/Cas12a trans-cleavage activity, enabling the establishment of a one-step detection system. The one-step Fast-Flu system demonstrated the ability to specifically identify Flu B within 45 min, with a limit of detection of 58 copies per test. It eliminates the need for uncapping operations and minimizes the risk of cross-contamination, without cross-reactivity with other pathogens. When evaluated using 101 clinical throat swab samples, the one-step Fast-Flu system achieved a sensitivity of 56.25% and a specificity of 100% compared to the PCR-based method, with an overall concordance rate of 93.06% (94/101). The development of this one-step RT-RPA-CRISPR/Cas12a system represents a significant advancement in the rapid, convenient, and accurate detection of Flu B, highlighting its potential for clinical diagnosis. Furthermore, with future technical improvements to enhance sensitivity, this one-step RT-RPA-CRISPR assay holds promise as a versatile tool for the rapid nucleic acid detection of other RNA viruses.

IMPORTANCE

Influenza B virus (Flu B) is a significant global health concern, and rapid, accurate pathogen diagnosis is crucial for effective influenza prevention and control. The integration of isothermal amplification methods with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has achieved high sensitivity and specificity for nucleic acid detection. Although CRISPR/Cas-based systems have been developed for influenza detection, existing platforms require the transfer of amplified products into the CRISPR/Cas12a detection system through uncapping operations, which increases the risk of cross-contamination. In this study, we developed a one-step reverse transcription recombinase polymerase amplification-CRISPR/Cas12a Flu B detection method using a one-pot detection system. By optimizing the reaction temperature and Cas12a concentration, we achieved a streamlined and contamination-free workflow. This innovative approach not only improves Flu B detection but also serves as a valuable reference for constructing CRISPR/Cas systems for the detection of other pathogens and targets, paving the way for broader applications in molecular diagnostics.

A Primer-Regulated Rolling Circle Amplification (RCA) for Logic-Controlled Multiplexed Enzyme Analysis

DNA-related enzymes are associated with various diseases and have been potential biomarkers for clinical diagnosis. Developing robust and ultrasensitive methods is extremely favorable for the detection of these biomarkers. To this purpose, a primer-regulated rolling circle amplification (RCA) strategy was ingeniously proposed. Briefly, the RCA primer, which was invalidated with 3'-inverted dT (locked state) and unable to initiate an amplification reaction by phi29 DNA polymerase, was embedded with the recognition substrate of the specific enzyme. In the presence of the target, the recognition and cleavage process of the enzyme prompted the release of the 3'-inverted dT and the regeneration of 3'-OH (unlocked state), satisfying the vital prerequisite for RCA. By adopting this programmable and modular design, the recognition substrate can be either single base sites or a specific sequence for different types of enzymes. This also enables us to conduct single or multiple enzyme detection conveniently, relying on a logic-controlled manner including YES, OR, AND, and AND-OR operations. Overall, the proposed strategy is uniquely insightful and provides a universal tool for multiple analyses of diverse DNA-related enzymes.

Application and development of CRISPR-Cas12a methods for the molecular diagnosis of cancer: A review

Rapid, sensitive, and specific molecular detection methods are crucial for diagnosing, treating and prognosing cancer patients. With advancements in biotechnology, molecular diagnostic technology has garnered significant attention as a fast and accurate method for cancer diagnosis. CRISPR-Cas12a (Cpf1), an important CRISPR-Cas family member, has revolutionized the field of molecular diagnosis since its introduction. CRISPR-Cas technologies are a new generation of molecular tools that are widely used in the detection of pathogens, cancers, and other diseases. Liquid biopsy methods based on CRISPR-Cas12a have demonstrated remarkable success in cancer diagnosis, encompassing the detection of DNA mutations, DNA methylation, tumor-related viruses, and non-nucleic acid molecule identification. This review systematically discusses the developmental history, key technologies, and principles of CRISPR-Cas12a-based molecular diagnostic techniques and their applications in cancer diagnosis. This review has also discussed the future development directions of CRISPR-Cas12a, aiming for it to become a reliable new technology that can be used in clinical application.

Recent Advances in the CRISPR/Cas-Based Nucleic Acid Biosensor for Food Analysis: A Review

Food safety is a major public health issue of global concern. In recent years, the CRISPR/Cas system has shown promise in the field of molecular detection. The system has been coupled with various nucleic acid amplification methods and combined with different signal output systems to develop a new generation of CRISPR/Cas-based nucleic acid biosensor technology. This review describes the design concept of the CRISPR/Cas-based nucleic acid biosensor and its application in food analysis. A detailed overview of different CRISPR/Cas systems, signal amplification methods, and signal output strategies is provided. CRISPR/Cas-based nucleic acid biosensors have the advantages of high sensitivity, strong specificity, and timeliness, achieving fast analysis of a variety of targets, including bacteria, toxins, metal ions, pesticides, veterinary drugs, and adulteration, promoting the development of rapid food safety detection technology. At the end, we also provide our outlook for the future development of CRISPR/Cas-based nucleic acid biosensors.

Detection of Parasites in the Field: The Ever-Innovating CRISPR/Cas12a

The rapid and accurate identification of parasites is crucial for prompt therapeutic intervention in parasitosis and effective epidemiological surveillance. For accurate and effective clinical diagnosis, it is imperative to develop a nucleic-acid-based diagnostic tool that combines the sensitivity and specificity of nucleic acid amplification tests (NAATs) with the speed, cost-effectiveness, and convenience of isothermal amplification methods. A new nucleic acid detection method, utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease, holds promise in point-of-care testing (POCT). CRISPR/Cas12a is presently employed for the detection of Plasmodium falciparum, Toxoplasma gondii, Schistosoma haematobium, and other parasites in blood, urine, or feces. Compared to traditional assays, the CRISPR assay has demonstrated notable advantages, including comparable sensitivity and specificity, simple observation of reaction results, easy and stable transportation conditions, and low equipment dependence. However, a common issue arises as both amplification and cis-cleavage compete in one-pot assays, leading to an extended reaction time. The use of suboptimal crRNA, light-activated crRNA, and spatial separation can potentially weaken or entirely eliminate the competition between amplification and cis-cleavage. This could lead to enhanced sensitivity and reduced reaction times in one-pot assays. Nevertheless, higher costs and complex pre-test genome extraction have hindered the popularization of CRISPR/Cas12a in POCT.