Rapid and sensitive exosome detection with CRISPR/Cas12a

GO-aptamer hydrogel microneedle sensors for the on-site detection of exosomes in interstitial fluid on acupuncture treatment

Acupuncture treatment had achieved good clinical effects on treat or ameliorate chronic diseases. Exosomes are crucial for transmitting information and network regulation in acupuncture, and their content could be essential for acupuncture's effects. However, there remains a critical need for a highly sensitive approach to detect exosomes in acupuncture therapy studies, particularly for rapid and precise analysis. Herein, a graphene oxide-aptamer hydrogel microneedle sensor (GOA-HMS) was designed for exosome point of care testing (POCT) on acupuncture treatment. The sensor was fabricated by cross-linking of aminophenylboronic acid (APBA)-modified sodium alginate with chondroitin sulfate and GO nanosheets conjugated with a fluorophore-modified nucleic acid aptamer, in which GO served as a quencher. In the absence of the target exosome, the aptamer binds tightly into the GO, quenching the fluorophore labels. In the presence of exosome, the aptamer binds to the targets, causing a conformational change which alters the distance the fluorescent moieties from the GO, leading to fluorescence recovery and the generation of fluorescent signals. This sensor showed a linear range of 105-109 particles/mL and has a detection limit of 1 particles/mL with an excellent precision of 4.3 % (RSD) for seven repeated detections of 107 particles/mL exosome, demonstrating the feasibility of both point-of-care clinical diagnostics and high throughput. Meanwhile, typical enzyme-linked immunosorbent assay (ELISA) assay further verified the measurement accuracy by this GOA-HMS. The GOA-HMS was successfully applied to exosome detection in acupuncture treatment, providing a non-invasive, in situ tool for monitoring patient responses in real-time and investigating acupuncture mechanisms.

"Sample-in, result-out" liquid biopsy chip based on immunomagnetic separation and CRISPR detection for multiplex analysis of exosomal microRNAs

Multiplex analysis of exosomal microRNAs (miRNAs) plays an important role in noninvasive early disease diagnosis. However, the complexity of the testing process has hindered its clinical application. Here, we proposed an integrated chip for the detection of eight exosomal miRNAs in serum which can achieve "sample in, result out" detection. We developed an immunomagnetic isolation system based on CD63 aptamers (IISA) for separation of serum exosomes. The system was combined with immiscible filtration assisted by surface tension (IFAST) to remove impurities. Bubble mixing was applied to ensure adequate binding or cleavage of exosomes to magnetic beads. CRISPR detection technology was utilized to allow for effective detection of seven hepatocellular carcinoma (HCC)-related miRNA targets. Based on the test of clinical samples, the chip can achieve 78 % exosome capture efficiency and 55 % recovery, and simultaneously detect eight targets within 1 h. This chip could be applied as a robust and cost-effective tool for cancer diagnosis and monitoring of cancer stages.

Theranostic potential of extracellular vesicles in reproductive tracts: implications for recurrent implantation failure

Embryo implantation is a critical step at the beginning of pregnancy, occurring during a specific and limited period known as the "implantation window". Successful implantation involves various signaling pathways and molecular interactions. Recent studies have highlighted the importance of extracellular vesicles (EVs) in mediating these complex interactions. Different cell types release EVs to transfer signals to other cells or tissues. Additionally, emerging evidence suggests that EVs regulate signaling between the developing embryo and endometrium. In this review, we summarize current findings that highlight the role of EVs in the reproductive tract, gamete production, and their potential roles in embryo development and implantation. We then examine studies emphasizing the role of EVs in embryo-maternal interactions and implantation. Finally, we will explore the theranostic potential of EVs in various aspects of assisted reproductive technology (ART), including modulation of embryo-maternal interactions, enhancement of embryo quality, and improvement of endometrial receptivity. A more comprehensive understanding of EVs in the pathology of recurrent implantation failure could support the development of personalized treatments.

Target-induced proximity ligation triggers polymerase chain reaction for subset tracing of small extracellular vesicles

The considerable abundance and remarkable stability of sEVs provide substantial benefits for diagnosing Alzheimer's disease. Therefore, precise tracking subtypes of small extracellular vesicles (sEVs) is crucial for screening novel diagnostic biomarkers and developing therapeutic technologies. We propose a three-target recognition-mediated proximity ligation assay for the precise identification of sEV subtypes utilizing three specifically designed probes: one for the exosomal surface protein CD63 recognition, one for fixing the biolipid layer, and the third for the identification of distinctive protein associated with a specific subtype of sEVs (L1CAM positive sEVs). The developed sEVs subtype tracing approach integrates proximity ligation of the three probes to specifically bind to surface biomarkers and polymerase chain reaction (PCR) for signal amplification, enabling "AND" logic analysis of three essential components on sEVs. This method can be utilized for both sEVs quantification and subtype tracing. The proposed approach demonstrated a low limit of detection for neuronal sEVs at 2.5 particles/μL, according to this design. In addition, we utilized this technique to measure plasma sEV levels in individuals with Alzheimer's disease and examined its early diagnostic effectiveness. The approach can assess the concentration ratios of neuronal sEVs and cancer-derived sEVs, highlighting its potential for clinical applications. In addition, the approach enables precise tracing and identification of sEVs subtypes, hence facilitating extensive applications in biological science, biomedical engineering, and personalized medicine.

CRISPR-based non-nucleic acid detection

Characterization of clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) trans-cleavage activities has initiated the era of next-generation CRISPR diagnostics. By using the trans-cleavage reaction for signal output, CRISPR systems have been engineered to detect non-nucleic acids (NNAs), including ions, inorganic small molecules, organic compounds, proteins, and bacteria. Diverse strategies are being used to specifically recognize NNAs and regulate Cas trans-cleavage activities, via generation or depletion of output signals. In this review, we introduce the principles and advantages of CRISPR-based NNA detection. We then classify CRISPR-based NNA detection strategies into three classes: the generation or depletion of free activators, synthesis of crRNAs, and reconstruction of active Cas effectors. Finally, we discuss the challenges and potential strategies to advance both clinical and nonclinical applications of CRISPR-based NNA detection.

A Versatile Colorimetric Diagnostic Platform Based on Primer Exchange Reaction Cascades Driven Loop-Mediated Isothermal Amplification

The primer exchange reaction (PER), as a well-established and sophisticated isothermal nucleic acid amplification strategy, has been extensively employed to amplify various genetic biomarkers. However, the amplification efficiency of conventional PER is generally unsatisfactory due to its linear signal-amplifying mechanism. In this study, we developed a versatile colorimetric platform by rationally integrating Primer exchange reaction with efficient Loop-mediated isothermal amplification (LAMP), termed vcPeLa, for the rapid and sensitive detection of cancer-related biomarkers, such as microRNAs (miRNAs) and carcinoembryonic antigen (CEA). The PER cascade in the vcPeLa can be directly initiated by the target, resulting in the production of long single-stranded DNA products with repeated functional sections. These repeats in the product can serve as the template to produce a significant number of double stem-loop DNAs with the cooperation of DNA polymerase and hairpin structure primer probes. These DNAs are the primary starting materials for subsequent LAMP. A substantial quantity of pyrophosphate can be recognized by Cu2+-chelated pp Probe (pyrophosphate sensing probe). The Cu2+ is removed from the Cu2+-chelated pp Probe as a result of the formation of a complex between Cu2+ and pyrophosphate, which results in color changes. Consequently, the vcPeLa platform is feasible to detect 0.31 fM miRNA and 0.043 ng/mL CEA with high selectivity and stability without the requirement of introducing any additional reaction steps or sample transfer operations in comparison to conventional assays. Therefore, this facile and ultrasensitive vcPeLa platform provides a new promising tool for cancer diagnosis and biomarker screening.

Engineering stimuli-responsive CRISPR-Cas systems for versatile biosensing

The precise target recognition and nuclease-mediated effective signal amplification capacities of CRISPR-Cas systems have attracted considerable research interest within the biosensing field. Guided by insights into their structural and biochemical mechanisms, researchers have endeavored to engineer the key biocomponents of CRISPR-Cas systems with stimulus-responsive functionalities. By the incorporation of protein/nucleic acid engineering techniques, a variety of conditional CRISPR-Cas systems whose activities depend on the presence of target triggers have been established for the efficient detection of diverse types of non-nucleic acid analytes. In this review, we summarized recent research progress in engineering Cas proteins, guide RNA, and substrate nucleic acids to possess target analyte-responsive abilities for diverse biosensing applications. Furthermore, we also discussed the challenges and future possibilities of the stimulus-responsive CRISPR-Cas systems in versatile biosensing.

A dCas9/sgRNA complex-mediated competitive assay for accurate and sensitive Pseudomonas aeruginosa analysis

Pseudomonas aeruginosa (P. aeruginosa), a Gram-negative pathogenic bacterium, is one of the most common bacteria that causes severe infectious diseases. However, accurate and efficient detection of P. aeruginosa in clinical samples is a huge challenge. Therefore, in this study, we developed a Cas9 derivative (dCas9)/sgRNA-mediated competitive assay for the sensitive and precise characterization of genomic materials from P. aeruginosa. Our approach involved the identification of target genomic sequences using the dCas9/sgRNA complex, which occupied the "sensing probe" (SP) binding site, resulting in an increased availability of free SP. SP subsequently facilitated DNA polymerase/endonuclease-mediated signal cycles and signal production, enabling highly sensitive detection of P. aeruginosa. The proposed competitive assay demonstrated a robust linear response to P. aeruginosa within a concentration range from 10 CFU mL-1 to 106 CFU mL-1, leveraging numerous signal amplification processes and competitive target recognition while exhibiting robust anti-interference capacity. Compared with former strategies, the proposed competitive assay enabled the accurate detection of P. aeruginosa by directly identifying and binding genomic sequences, which could be easily extended to the detection of other bacteria by simply changing the sgRNA. In addition, the proposed approach exhibits significant clinical potential for early disease diagnosis owing to its excellent sensitivity and accuracy.

CRISPR integrated biosensors: A new paradigm for cancer detection

Cancer remains one of the leading causes of morbidity and mortality globally, necessitating need for advancements of technologies for early therapeutics. Conventional detection methodologies often lag behind in terms of sensitivity, specificity, and cost-effectiveness, leading to delayed diagnosis and inadequate treatment. The need of advanced diagnostic techniques has considerably increased and led to the development of biosensors. Biosensing technologies offer several advantages over conventional methods hence, overcome limitations and improve diagnostic accuracy. Biosensors, particularly CRISPR-Cas based biosensors have emerged as a revolutionary technology for oncology diagnostics due to their high precision and adaptability. CRISPR-based biosensors provide remarkable precision, sensitivity, multiplexing capabilities, specificity, and rapidness for developing a cost-effective and portable point of care diagnostic device for cancer detection. In this review, we have discussed cancer pathogenicity, assessed the traditional detection techniques, and explored the advancements and advantages of biosensors, particularly CRISPR-based biosensors, in the detection of some major cancer types, namely lung, liver, colorectal, prostate, and cervical cancers. CRISPR-based biosensors represent a significant potential in cancer diagnostics, offering precise, cost-effective, and rapid detection of cancer biomarkers. The integration of CRISPR technology with biosensors holds substantial promise for enhancing early detection and improving patient outcomes in cancer diagnostics.

Synthetic biology meets Aspergillus: engineering strategies for next-generation organic acid production

Organic acids constitute a vital category of chemical raw materials. They have extensive applications in industries such as polymers, food, and pharmaceuticals. Currently, industrial production predominantly relies on microbial fermentation. Aspergillus, due to its unique metabolic capabilities, has become an important microbial resource for organic acid production. In recent years, there has been a growing emphasis on genetic engineering of Aspergillus to increase its yield of organic acids. This review provides a comprehensive overview of the current advancement and future directions in the application of genetic engineering techniques to enhance organic production in Aspergillus, specifically highlighting achievement in reconstructing metabolic pathways for desired products, eliminating by-products, modifying regulatory pathways, and engineering mycelial morphology. Furthermore, this review also focuses on the strategies and genetic tools applied in Aspergillus, with particular emphasis on the potential applications and challenges of CRISPR-based biosensors in organic acid fermentation. By providing insights into these developments, we aim to offer theoretical guidance and innovative approaches for enhancing the efficiency of Aspergillus strains in industrial organic acid production.

Recent progress in prompt molecular detection of liquid biopsy using Cas enzymes: innovative approaches for cancer diagnosis and analysis

Creating fast, non-invasive, precise, and specific diagnostic tests is crucial for enhancing cancer treatment outcomes. Among diagnostic methods, those relying on nucleic acid detection are highly sensitive and specific. Recent developments in diagnostic technologies, particularly those leveraging Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are revolutionizing cancer detection, providing accurate and timely results. In clinical oncology, liquid biopsy has become a noninvasive and early-detectable alternative to traditional biopsies over the last two decades. Analyzing the nucleic acid content of liquid biopsy samples, which include Circulating Tumor Cells (CTCs), Circulating Tumor DNA (ctDNA), Circulating Cell-Free RNA (cfRNA), and tumor extracellular vesicles, provides a noninvasive method for cancer detection and monitoring. In this review, we explore how the characteristics of various Cas (CRISPR-associated) enzymes have been utilized in diagnostic assays for cancer liquid biopsy and highlight their main applications of innovative approaches in monitoring, as well as early and rapid detection of cancers.

A catalytic assembly triggered DNAzyme motor on spherical nucleic acids for sensitive small extracellular vesicle detection

The expression levels of small extracellular vesicles (sEVs) are closely associated with several significant biological processes, which can be used as a crucial biomarker for cancer diagnosis, such as colorectal cancer. More efforts are still necessary to amplify sEV detection sensitivity, as their expression is minimal during the early stages of colorectal cancer. Through the integration of a catalytic assembly-triggered DNAzyme motor and gold nanoparticle (AuNP) aggregation, we have developed a triple signal amplified biosensor for the detection of sEVs. In this method, the catalytic assembly triggered DNAzyme motor continuously cleaved on the hairpin probe which is fixed on the surface of AuNPs, leaving a single-stranded sequence on the surface of AuNPs to induce the aggregation. This approach employs a triple signal amplification process to enhance the efficiency of the reaction and circumvent the issue of expensive and readily degradable proteases. The signal output system is based on dynamic light scattering technology, which enables ultra-sensitive detection of sEVs with a detection limit of 3.08 particles per μL. The present strategy exhibits significant potential for the analysis of a variety of additional analytes in clinical research disciplines due to its appealing analytical capabilities.

Immobilization coupling with aptamer assisted dual cycle amplification for sensitive sEVs isolation and analysis

Precise identification of small extracellular vesicles (sEVs) is crucial for improving disease diagnosis and treatments, such as bladder cancer. However, accurate isolation and simultaneously quantification of sEVs remain a huge challenge. We have introduced a new technique that combines immobilization with aptamer-assisted dual cycle amplification to isolate and analyze sEVs with high sensitivity. In this method, the CD9 protein antibody is attached to the plate's surface for the initial identification of sEVs, while an aptamer probe is used to detect the exosomal surface protein CD63. We have created an sEVs-surface method that combines target recognition initiated signal recycling and rolling circle amplification (RCA) for signal amplification. This approach allows for the "AND" logic analysis of dual biomarkers, enabling both sEVs quantification and tracing. The proposed approach has a broad detection range and a low limit of detection. Moreover, the established method showed good stability in detecting sEVs with a low coefficient of variation. Our method can effectively isolate certain sEVs and accurately identify them, making it suitable for many uses in biological science, biomedical engineering, and personalized medicine.

A chemiluminescent sensor based on CRISPR-HCR technology for the hypersensitive detection of Mycobacterium tuberculosis

Tuberculosis is a highly infectious bacterial disease caused by Mycobacterium tuberculosis. The spread of this agent has caused serious health problems worldwide, and the rapid and accurate detection of M. tuberculosis is essential for controlling the spread of infection and for preventing the emergence of multidrug-resistant strains. In this study, the trans cleavage ability of CRISPR-Cas12a against single-stranded DNA was combined with hybridization chain reaction and chemiluminescent signal to establish an imaging sensor for the hypersensitive detection of M. tuberculosis DNA. We observed linear relationships between the concentration of M. tuberculosis DNA and the output signal over the ranges of 10 to 200 pM and 200 to 800 pM DNA. The equations of the standard curves were y = 56.08x + 3303, with R2 = 0.9916 for the lower range and y = 15.69x + 10 685, with R2 = 0.9929 for the higher range. The limit of detection was as low as 0.83 pM for genomic DNA, and a plasmid containing an M. tuberculosis-specific sequence was detected at 1 copy per μL. A detection accuracy of 100% was achieved in the analysis of DNA isolated from sputum of hospitalized tuberculosis patients. The sensitivity and specificity of the proposed sensor is combined with a long shelf-life and a low cost of materials. This study introduces a new method for tuberculosis detection and broadens the application of CRISPR-Cas12a-based sensors in clinical diagnosis.

Recent developments in antibiotic resistance: an increasing threat to public health

Antibiotic resistance (ABR) is a major global health threat that puts decades of medical progress at risk. Bacteria develop resistance through various means, including modifying their targets, deactivating drugs, and utilizing efflux pump systems. The main driving forces behind ABR are excessive antibiotic use in healthcare and agriculture, environmental contamination, and gaps in the drug development process. The use of advanced detection technologies, such as next-generation sequencing (NGS), clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics, and metagenomics, has greatly improved the identification of resistant pathogens. The consequences of ABR on public health are significant, increased mortality rates, the endangerment of modern medical procedures, and resulting in higher healthcare expenses. It has been expected that ABR could potentially drive up to 24 million individuals into extreme poverty by 2030. Mitigation strategies focus on antibiotic stewardship, regulatory measures, research incentives, and raising public awareness. Furthermore, future research directions involve exploring the potential of CRISPR-Cas9 (CRISPR-associated protein 9), nanotechnology, and big data analytics as new antibiotic solutions. This review explores antibiotic resistance, including mechanisms, recent trends, drivers, and technological advancements in detection. It also evaluates the implications for public health and presents strategies for mitigating resistance. The review emphasizes the significance of future directions and research needs, stressing the necessity for sustained and collaborative efforts to tackle this issue.

Raman-enhanced sensor based on CRISPR-SERS technology for the rapid and hypersensitive detection of Mycobacterium tuberculosis

Tuberculosis is a highly infectious disease caused by the bacterium Mycobacterium tuberculosis, and the spread of this agent has caused serious health problems worldwide. The rapid and accurate detection of M. tuberculosis is essential for controlling the spread of infection and for preventing the emergence of multidrug-resistant strains. In this study, the powerful trans-cleavage ability of CRISPR-Cas12a for ssDNA was combined with a surface-enhanced Raman spectroscopy (SERS)-based strategy to establish a CRISPR-SERS sensor for the hypersensitive detection of M. tuberculosis DNA. We observed a linear relationship between the concentration of M. tuberculosis DNA and the output signal over the range of 5 to 100 pM. The equation describing the standard curve was y = 24.10x + 1594, with R2 = 0.9914. The limit of detection was as low as 4.42 pM for genomic DNA, and a plasmid containing an M. tuberculosis-specific sequence was detected at 5 copy/μL. A detection accuracy of 100% was achieved in the analysis of DNA isolated from the sputum of hospitalized patients with tuberculosis. The entire detection process is simple to deploy and only takes 50 min and results in the sensitive and specific detection of M. tuberculosis DNA. This study provides a new method for the detection of tuberculosis. The tool is stable and can be utilized on-site, and it thus broadens the diagnostic application of CRISPR-Cas12a-based sensor technology.

CRISPR-Cas-based biosensors for the detection of cancer biomarkers

Along with discovering cancer biomarkers, non-invasive detection methods have played a critical role in early cancer diagnosis and prognostic improvement. Some traditional detection methods have been used for detecting cancer biomarkers, but they are time-consuming and involve materials and human costs. With great flexibility, sensitivity and specificity, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated system provides a wide range of application prospects in this field. Herein, we introduce the background of the CRISPR-Cas (CRISPR-associated) system and comprehensively summarize the diagnosis strategies of cancer mediated by the CRISPR-Cas system, including four kinds of biochemical-based markers: nucleic acid, enzyme, tumor-specific protein and exosome. Furthermore, we discuss the challenges in implementing the CRISPR-Cas system in clinical applications.

Sensitive and Enzyme-Free Pseudomonas aeruginosa Detection and Isolation via DNAzyme Cascade Triggered DNA Tweezer

Effective isolation and sensitive detection of Pseudomonas aeruginosa (P. aeruginosa) is crucial for the early diagnosis and prognosis of various diseases, such as urinary tract infections. However, efficient isolation and simultaneous detection of P. aeruginosa remains a huge challenge. Herein, we depict a novel fluorescence assay for sensitive, enzyme-free detection of P. aeruginosa by integrating DNAzyme cascade-induced DNA tweezers and magnetic nanoparticles (MNPs)-based separation. The capture probe@MNPs is capable of accurately identifying target bacteria and transporting the bacteria signal to nucleic acid signals. Based on the DNAzyme cascade-induced DNA tweezers, the nucleic acid signals are extensively amplified, endowing the method with a high sensitivity and a low detection limit of 1 cfu/mL. In addition, the method also exhibits a wide detection of six orders of magnitudes. The proposed method could be extended to other bacteria detection by simply changing the aptamer sequence. Taking the merit of the high sensitivity, greatly minimized detection time (less than 1.5 h), enzyme-free characteristics, and stability, the proposed method could be potentially applied to diagnosing and preventing diseases caused by pathogenic bacteria.

CRISPR-Driven Biosensors: A New Frontier in Rapid and Accurate Disease Detection

This comprehensive review delves into the advancements and challenges in biosensing, with a strong emphasis on the transformative potential of CRISPR technology for early and rapid detection of infectious diseases. It underscores the versatility of CRISPR/Cas systems, highlighting their ability to detect both nucleic acids and non-nucleic acid targets, and their seamless integration with isothermal amplification techniques. The review provides a thorough examination of the latest developments in CRISPR-based biosensors, detailing the unique properties of CRISPR systems, such as their high specificity and programmability, which make them particularly effective for detecting disease-associated nucleic acids. While the review focuses on nucleic acid detection due to its critical role in diagnosing infectious diseases, it also explores the broader applications of CRISPR technology in detecting non-nucleic acid targets, thereby acknowledging the technology's broader potential. Additionally, the review identifies existing challenges, such as the need for improved signal amplification and real-world applicability, and offers future perspectives aimed at overcoming these hurdles. The ultimate goal is to advance the development of highly sensitive and specific CRISPR-based biosensors that can be used widely for improving human health, particularly in point-of-care settings and resource-limited environments.

CRISPR/Cas12a and aptamer-chemiluminescence based analysis for the relative abundance determination of tumor-related protein positive exosomes for breast cancer diagnosis

Exosomes, as novel biomarker for liquid biopsy, exhibit huge important potential value for cancer diagnosis. However, various proteins show different expression levels on exosomal membrane, and the absolute concentration of exosomes in clinical samples is easily influenced by a number of factors. Here, we developed a CRISPR/Cas12a and aptamer-chemiluminescence based analysis (CACBA) for the relative abundance determination of tumor-related protein positive exosomes in plasma for breast cancer diagnosis. The total concentration of exosomes was determined through captured CD63 using a CRISPR/Cas12a-based method with the LoD of 8.97 × 103 particles/μl. Meanwhile, EpCAM and MUC1 positive exosomes were quantitatively detected by aptamer-chemiluminescence (ACL) based method with the LoD of 1.45 × 102 and 3.73 × 102 particles/μl, respectively. It showed that the percentages of EpCAM and MUC1 positive exosomes offered an excellent capability to differentiate breast cancer patients and healthy donors. The high sensitivity, strong specificity, outstanding anti-interference capability, and steady recovery rate of this approach offered higher accuracy and robustness than the commercialized method in clinical trial. In addition with good stability, easy preparation and low cost, this method not only provides a new approach to rapid analysis of exosome proteins, it may be quickly extended to the diagnoses of various cancers.

CRISPR-Cas Systems: Programmable Nuclease Revolutionizing the Molecular Diagnosis

CRISPR-Cas system has evolved as a highly preferred genetic engineering tool to perform target gene manipulation via alteration of the guide RNA (gRNA) sequence. The ability to recognize and cleave a specific target with high precision has led to its applicability in multiple frontiers pertaining to human health and medicine. From basic research focused on understanding the molecular basis of disease to translational approach leading to early and precise disease diagnosis as well as developing effective therapeutics, the CRISPR-Cas system has proved to be a quite versatile tool. The coupling of CRISPR-Cas mediated cleavage with isothermal amplification (ISA) of target DNA, followed by a read-out using fluorescent or colorimetric reporters appears quite promising in providing a solution to the urgent need for nucleic acid-based point-of-care diagnostic. Hence, it has been recognized as a highly sophisticated molecular diagnostic tool for the detection of disease-specific biomarkers not limited to nucleic acids-based detection but also of non-nucleic acid targets such as proteins, exosomes, and other small molecules. In this review, we have presented salient features and principles of class 2 type II, V, and VI CRISPR-Cas systems represented by Cas9, Cas12, and Cas13 endonucleases which are frequently used in molecular diagnosis. The article then highlights different medical diagnostic applications of CRISPR-Cas systems focusing on the diagnosis of SARS-CoV-2, Dengue, Mycobacterium tuberculosis, and Listeria monocytogenes. Lastly, we discuss existing obstacles and potential future pathways concerning this subject in a concise manner.

CRISPR/Cas12a-Based APE1 Enzyme Cleavage Assay for Drug Resistance Analysis of Staphylococcus aureus-Related Pneumonia

Drug resistance analysis of Staphylococcus aureus is responsible for generating significant mortality and morbidity in numerous diseases. However, sensitive and accurate analysis of drug resistance of S. aureus remains a huge challenge. In this study, we present the development of a fluorescence biosensor based on the CRISPR/Cas12a system that enables label-free and ultrasensitive detection of the mecA gene in methicillin-resistant S. aureus (MRSA). The biosensor identified the mecA gene in MRSA using Cas12a/crRNA. This recognition triggered the trans-cleavage activity of Cas12a and the release of RNA1, which subsequently induced Apurinic/apyrimidinic endonuclease 1 (APE1) enzyme-assisted target recycling and G-quadruplexes/Thioflavin T-based signal reaction. Based on this, the biosensor effectively detects the mecA gene with a low limit of detection of 212 aM and a high degree of selectivity, even toward single base mutations. Compared with the traditional CRISPR-Cas12a system-based methods, in which the signal amplification process is prone to generate nucleic acid sequence mismatch, which causes errors, the biosensor used APE1 to improve nucleic acid sequence recognition specificity to ensure that the RNA1 sequence released after Cas12a/crRNA cleavage can specifically guide the signal cycle. In addition to enhancing the CRISPR toolkit, the developed biosensor offers a novel method for the precise and sensitive identification of drug-resistant microbes that cause infections.

A proximity ligation hybridization triggered structure-switching based signal amplification strategy for sensitive and accurate exosome detection

Exosomes have significant functions in intercellular communication, as well as in tumor migration and invasion. Nevertheless, the precise identification of exosomes poses a significant obstacle due to their low abundance in biofluids and potential disruption caused by free protein molecules, such as CD63 protein. In this study, we have developed a signal amplification method for precise detection of exosomes using a proximity ligation hybridization triggered structure-switching approach. The method involves the dual-recognition of exosomes by two probes: an aptamer probe that recognizes the exosomal surface protein CD63 (L1 probe), and a cholesterol probe that targets the biolipid layer of the exosomes (L2 probe). Based on the dual-recognition of exosomes, we have successfully developed an accurate and sensitive approach that integrates the proximity ligation hybridization technique with a structure-switching based signal cycle. This approach allows for the simultaneous analysis of two biomarkers, enabling both quantification and tracing of exosomes without the need for enzymes. Eventually, the proposed method exhibits a wide detection range of 5 orders of magnitude and a low limit of detection of 36 particles per μL, making it suitable for a wide range of applications in the fields of biological science, biomedical engineering, and personalized medicine.

APPROACH: Sensitive Detection of Exosomal Biomarkers by Aptamer-Mediated Proximity Ligation Assay and Time-Resolved Förster Resonance Energy Transfer

Exosomal biomarker detection holds great importance in the field of in vitro diagnostics, offering a non-invasive and highly sensitive approach for early disease detection and personalized treatment. Here, we proposed an "APPROACH" strategy, combining aptamer-mediated proximity ligation assay (PLA) with rolling circle amplification (RCA) and time-resolved Förster resonance energy transfer (TR-FRET) for the sensitive and semi-homogenous detection of exosomal biomarkers. PLA probes consisted of a cholesterol-conjugated oligonucleotide, which anchored to the membrane of an exosome, and a specific aptamer oligonucleotide that recognized a target protein of the exosome; the proximal binding of pairs of PLA probes to the same exosome positioned the oligonucleotides in the vicinity of each other, guiding the hybridization and ligation of two subsequently added backbone and connector oligonucleotides to form a circular DNA molecule. Circular DNA formed from PLA underwent rolling circle amplification (RCA) for signal amplification, and the resulting RCA products were subsequently quantified by TR-FRET. The limits of detection provided by APPROACH for the exosomal biomarkers CD63, PD-L1, and HER2 were 0.46 ng∙μL-1, 0.77 ng∙μL-1, and 1.1 ng∙μL-1, respectively, demonstrating excellent analytical performance with high sensitivity and quantification accuracy. Furthermore, the strategy afforded sensitive detection of exosomal CD63 with a LOD of 1.56 ng∙μL-1 in complex biological matrices, which underscored its anti-interference capability and potential for in vitro detection. The proposed strategy demonstrates wide-ranging applicability in quantifying diverse exosomal biomarkers while exhibiting robust analytical characteristics, including high sensitivity and accuracy.

CRISPR-Cas12a based target recognition initiated duplex-specific nuclease enhanced fluorescence and colorimetric analysis of cell-free DNA (cfDNA)

The significant role of cell-free DNA (cfDNA) for disease diagnosis, including cancer, has garnered a lot of attention. The challenges of creating target-specific primers and the possibility of false-positive signals make amplification-based detection methods problematic. Fluorescent biosensors based on CRISPR-Cas have been widely established, however they still require an amplification step before they can be used for detection. To detect cfDNA, researchers have created a CRISPR-Cas12a-based nucleic acid amplification-free fluorescent biosensor that uses a combination of fluorescence and colorimetric signaling improved by duplex-specific nuclease (DSN). DSN-assisted signal recycling is initiated in H1@MBs when the target cfDNA activates the CRISPR-Cas12a complex, leading to the degradation of single-strand DNA (ssDNA) sequences. This method has an extremely high detection limit for the BRCA-1 breast cancer gene. In addition to measuring viral DNA in a field-deployable and point-of-care testing (POCT) platform, this fast and highly selective sensor can be used to evaluate additional nucleic acid biomarkers.

Label-Free, Sensitive, and Versatile Colorimetric Method for Molecule Detection via the G-Quadruplex-Based Signal Quenching Strategy

Signal amplification strategies have emerged as a prominent tool in the field of improving the detection sensitivity of small extracellular vesicles (sEVs). It is important to highlight that the utilization of signal quenching strategies is not commonly implemented. A detection technique for sEVs was established based on the unwinding of G-quadruplex using Klenow fragment polymerase (KF), which served as an inspiration for this study. This system is characterized by its simplicity and lack of labeling, making it an efficient approach for signal quenching. In the presence of sEVs, the CD63 aptamer in the capture@sMBs complex binds with the CD63 protein on the surface of sEVs to release trigger sequences, which were employed as a primer to mediate the DNA polymerase/endonuclease-assisted signal recycling. The signal recycling process produces numerous single-stranded DNA sequences that can bind to the toehold section of the G-quadruplex. This leads to the rupture of the G-quadruplex structure and the subsequent deactivation of a DNAzyme generated by the G-quadruplex structure and hemin, thereby inhibiting its biological catalytic function. Consequently, the G-quadruplex structure would undergo a transformation to a duplex structure, leading to the emergence of a discernible differential signal that can be noticed in a majority of instances, even without the aid of magnification devices. The decrease in the prominent signal allows for the efficient analysis of target sEVs, which exhibit a notably low detection limit. In addition to the detection of sEVs, the approach has also been utilized for the investigation of miRNA-21. The approach demonstrates a high level of selectivity and robustness in its capacity to differentiate between target miRNA and base-mismatched miRNA as well as other miRNA families. This statement suggests that the assay holds significant promise for use in biochemical research and clinical diagnosis.

"DSN-mismatched CRISPR″sensor for highly selective and sensitive detection of under-expressed miR-let-7a

Several microRNAs (miRNAs) are expressed at lower levels in specific tumors, e.g., miR-let-7a in non-small cell lung cancer (NSCLC). This makes it challenging to analyze their lower abundance versus specifically elevated miRNAs. Here, we describe a novel fluorescent biosensor for the highly selective and sensitive detection of miR-let-7a constructed by combining miRNA screening assisted by a duplex-specific nuclease (DSN) with CRISPR-Cas12a system signal amplification. We meticulously designed a mismatch in the first three to four bases at the 5'-end of the capture DNA to improve the signal-to-noise ratio of the CRISPR-Cas12a system. Within this "DSN-mismatched CRISPR" fluorescence strategy, miR-let-7a was accurately screened by DSN-assisted cleavage, and the mismatched capture DNA unbound to target miRNA could trigger the CRISPR-Cas12a system to produce a mass of trans-cleave fluorescence signals. This "turn-off" approach was suitable for detecting decreased levels of miRNAs. This approach can not only discriminate the single-base mismatched let-7 family but also reach a limit of detection at 64.17 fM as well as be quantified from 100 fM to 500 pM. The miR-let-7a levels were then measured in clinical serum samples from healthy volunteers and patients with NSCLC. This study holds promise for the development of a universal under-expressed miRNA assay for early diagnosis and treatment of cancers.

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

Rapid, sensitive and selective biosensing is highly important for analyzing biological targets and dynamic physiological processes in cells and living organisms. As an emerging tool, clustered regularly interspaced short palindromic repeats (CRISPR) system is featured with excellent complementary-dependent cleavage and efficient trans-cleavage ability. These merits enable CRISPR system to improve the specificity, sensitivity, and speed for molecular detection. Herein, the structures and functions of several CRISPR proteins for biosensing are summarized in depth. Moreover, the strategies of target recognition, signal conversion, and signal amplification for CRISPR-based biosensing were highlighted from the perspective of biosensor design principles. The state-of-art applications and recent advances of CRISPR system are then outlined, with emphasis on their fluorescent, electrochemical, colorimetric, and applications in POCT technology. Finally, the current challenges and future prospects of this frontier research area are discussed.

Plug-and-play smart transistor bio-chips implementing point-of-care diagnosis of AMI with modified CRISPR/Cas12a system

The point-of-care diagnosis of acute myocardial infarction (AMI), an extremely lethal disease with only a few hours of golden rescue time, is significant and urgently required. Here, we describe a plug-and-play carbon nanotube field effect transistor (CNT-FET) bio-chip supported with a smart portable readout for ultrasensitive and on-site testing of cardiac troponin I (cTnI), which is one of the most specific and valuable biomarkers of AMI. A modified clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system, featuring the G-triplex structured reporter, was first combined with the CNT-FET to realize non-nucleic acid detection. Such a unique CNT-FET biosensor achieved the high sensitivity (LOD: 0.33 fg/mL), which is expected to give timely warning in the early stage of myocardial injury. In addition, a bilayer gate dielectric consisting of Y2O3/HfO2, employed into the passivation process, enabled the high environmental stability and repeatability of CNT-FET. More importantly, the homemade compact chip readout forged a field-deployable cTnI analytical tool, realizing "plasma-to-answer" performance for AMI patients in point-of-care testing scenarios. The developed technology holds promise to help doctors make clinical decisions faster, especially in remote areas.

DNA Gate-Based CRISPR-Cas Exponential Amplification System for Ultrasensitive Small Extracellular Vesicle Detection to Enhance Breast Cancer Diagnosis

Tumor-derived small extracellular vesicles (tEVs) as potential biomarkers possess abundant surface proteins closely related to parent cells, which are crucial for noninvasive cancer diagnosis. However, tEVs exhibit phenotype heterogeneity and low abundance, posing a significant challenge for multiplex detection with a high sensitivity. Herein, we developed a DNA gate-based exponential amplification CRISPR-Cas (DGEAC) system for accurate and ultrasensitive detection of tEVs, which can greatly improve the accuracy of breast cancer (BC) diagnosis. Based on the coexpression of CD63 and vascular endothelial growth factor (VEGF) on BC-derived tEVs, we developed a dual-aptamer-based AND gate fluorescent probe by proximity hybridization. By integrating the target recognition and trans-cleavage activity of Cas12a, an autocatalysis-driven exponential amplification circuit was developed for ultrasensitive detection of CD63 and VEGF proteins on tEVs, which could avoid false negative signals from single protein or other interfering proteins. We achieved highly sensitive detection of tEVs over a linear range from 1.75 × 103 to 3.5 × 108 particles/mL with a detection limit as low as 1.02 × 103 particles/mL. Furthermore, the DGEAC system can distinguish tEVs from tEVs derived from different BC cell lines, including MDA-MB-231, MCF-7, SKBR3, and MCF-10A. Compared to linear amplification (AUC 90.0%), the DGEAC system effectively differentiates BC in different stages (AUC 98.3%).

Enhancing CRISPR/Cas systems with nanotechnology

CRISPR/Cas systems have revolutionized biology and medicine, and have led to new paradigms in disease diagnostics and therapeutics. However, these complexes suffer from key limitations regarding barriers to cellular entry, stability in biological environments, and off-target effects. Integrating nanotechnology with CRISPR/Cas systems has emerged as a promising strategy to overcome these challenges and has further unlocked structures that accumulate preferentially in tissues of interest, have tunable pharmacological properties, and are activated in response to desired stimuli. Nanomaterials can also enhance CRISPR/Cas-mediated detection platforms by enabling faster, more sensitive, and convenient readouts. We highlight recent advances in this rapidly growing field. We also outline areas that need further development to fully realize the potential of CRISPR technologies.

Recent advances and challenges of the use of the CRISPR/Cas system as a non-nucleic acid molecular diagnostic

The clustered regularly interspaced short palindromic DNA sequence repeats (CRISPR) and CRISPR-associated (Cas) (CRISPR/Cas) systems are currently applied not only as a gene editing tool but also as a novel molecular diagnostic technique. The CRISPR/Cas systems have emerged as an efficient molecular diagnostic system that can detect nucleic acids, proteins and small molecule compounds, by converting a non-nucleic acid into a nucleic acid signal of Cas-identifiable and keeping inherent properties of high sensitivity and specificity. While its multiple advantages for nucleic acid detection have been widely published in excellent reviews, there have been no systematic analyses and reviews on the principles and characteristics of CRISPR/Cas-based diagnostic systems for non-nucleic acids. The present work reviewed the basic process, principles, characteristics, strategies, recent advances, and challenges of CRISPR/Cas-based molecular diagnostic methods for detecting non-nucleic acids, which may provide a basis or some references for future development and application as molecular diagnostic tools.

Emerging Microfluidic Tools for Simultaneous Exosomes and Cargo Biosensing in Liquid Biopsy: New Integrated Miniaturized FFF-Assisted Approach for Colon Cancer Diagnosis

The early-stage diagnosis of cancer is a crucial clinical need. The inadequacies of surgery tissue biopsy have prompted a transition to a less invasive profiling of molecular biomarkers from biofluids, known as liquid biopsy. Exosomes are phospholipid bilayer vesicles present in many biofluids with a biologically active cargo, being responsible for cell-to-cell communication in biological systems. An increase in their excretion and changes in their cargo are potential diagnostic biomarkers for an array of diseases, including cancer, and they constitute a promising analyte for liquid biopsy. The number of exosomes released, the morphological properties, the membrane composition, and their content are highly related to the physiological and pathological states. The main analytical challenge to establishing liquid biopsy in clinical practice is the development of biosensors able to detect intact exosomes concentration and simultaneously analyze specific membrane biomarkers and those contained in their cargo. Before analysis, exosomes also need to be isolated from biological fluids. Microfluidic systems can address several issues present in conventional methods (i.e., ultracentrifugation, size-exclusion chromatography, ultrafiltration, and immunoaffinity capture), which are time-consuming and require a relatively high amount of sample; in addition, they can be easily integrated with biosensing systems. A critical review of emerging microfluidic-based devices for integrated biosensing approaches and following the major analytical need for accurate diagnostics is presented here. The design of a new miniaturized biosensing system is also reported. A device based on hollow-fiber flow field-flow fractionation followed by luminescence-based immunoassay is applied to isolate intact exosomes and characterize their cargo as a proof of concept for colon cancer diagnosis.

A novel hydrophilic polymer-coated magnetic nanomaterial based on the HILIC strategy for fast separation of glycopeptides and glycosylated exosomes

Novel hydrophilic poly(N, N-methylenebisacrylamide/1,2-epoxy-5-hexene) coated magnetic nanospheres functionalized with 2-aminopurine (denoted as Fe3O4@poly(MBA/EH)@2AP) for enriching glycopeptides and glycosylated exosomes were successfully obtained using a simple and green method on the basis of the HILIC (hydrophilic interaction liquid chromatography) enrichment strategy. The high density of polar groups endows the material with amazing hydrophilicity, enabling the nanomaterial to successfully capture glycopeptides and glycosylated exosomes within 1 min. Meanwhile, the materials demonstrated great sensitivity (0.01 fmol/μL), good loading capability (125 μg/mg), high selectivity (BSA:HRP = 1000:1), and repeatability (more than 10 times). Besides, the material was applied in the analysis of bio-samples, a total of 290 glycosylated peptides and 184 glycosylation sites mapping to 185 glycoproteins were identified in the serum of uremic patients. Besides, 42 glycopeptides were enriched from the saliva of healthy people. At the same time, it was verified by TEM and western blot that the complete glycosylated exosomes were successfully captured from the serum of the uremic patients. All experiments have demonstrated that Fe3O4@poly(MBA/EH)@2AP has a promising future in practical applications.

A cathodic photoelectrochemical biosensor based on CRISPR/Cas12a trans-cleavage mediated p-n heterojunction quenching mode for microRNA determination

In this study, a cathodic photoelectrochemical (PEC) bioanalysis for sensitive determination of microRNA (miRNA) has been constructed based on CRISPR/Cas12a trans-cleavage mediated [(C6)₂Ir(dcbpy)]⁺PF₆^- (C6 represents coumarin-6 and dcbpy represents 4,4'-dicarboxyl-2,2'-bipyridine)-sensitized NiO photocathode and p-n heterojunction quenching mode. The [(C6)₂Ir(dcbpy)]⁺PF₆^--sensitized NiO photocathode exhibits a stable and dramatically improved photocurrent signal due to highly effective photosensitization of [(C6)₂Ir(dcbpy)]⁺ PF₆^-. Then Bi₂S₃ quantum dots (Bi₂S₃ QDs) is captured on the photocathode, resulting in markedly quenching of the photocurrent. When target miRNA is specifically recognized by the hairpin DNA to stimulate the trans-cleavage activity of CRISPR/Cas12a, leading to the leave of the Bi₂S₃ QDs. The photocurrent is gradually recovered with the increasing target concentration. Thus, the quantitative signal response to target is achieved. Benefiting from excellent performance of NiO photocathode, intense quenching effect of p-n heterojunction and accurate recognition ability of CRISPR/Cas12a, the cathodic PEC biosensor shows a wider linear range over 0.1 fM-10 nM, with a low detection limit of 36 aM. Also, the biosensor exhibits satisfying stability and selectivity.

Construction of a SERS platform for sensitive detection of aflatoxin B1 based on CRISPR strategy

Aflatoxin B1, a pathogen in the aflatoxin family, has attracted much attention due to the harmfulness in production and life. However, the common methods like high performance liquid chromatography used for detection of AFB1 have deficiency in complicated pretreatment processes, and the purification effect is not ideal. Herein, a SERS platform based on CRISPR strategy was designed for sensitive detection of AFB1. By synthesizing core-shell nanoparticles embedded with Raman silent region dye molecules, Prussian blue (PB), the detection of the sensor reduced background interference and the SERS signal was calibrated. At the same time, the high-efficiency reverse cleavage activity of cas12a was used to convert non-nucleic acid targets into nucleic acid, so as to achieve the effect of sensitive detection of AFB1 with a detection limit of 3.55  pg/mL. This study provides a new thought for SERS detection of non-nucleic acid targets in the future.

CRISPR/Cas9 Genome Editing for Tissue-Specific In Vivo Targeting: Nanomaterials and Translational Perspective

Clustered randomly interspaced short palindromic repeats (CRISPRs) and its associated endonuclease protein, i.e., Cas9, have been discovered as an immune system in bacteria and archaea; nevertheless, they are now being adopted as mainstream biotechnological/molecular scissors that can modulate ample genetic and nongenetic diseases via insertion/deletion, epigenome editing, messenger RNA editing, CRISPR interference, etc. Many Food and Drug Administration-approved and ongoing clinical trials on CRISPR adopt ex vivo strategies, wherein the gene editing is performed ex vivo, followed by reimplantation to the patients. However, the in vivo delivery of the CRISPR components is still under preclinical surveillance. This review has summarized the nonviral nanodelivery strategies for gene editing using CRISPR/Cas9 and its recent advancements, strategic points of view, challenges, and future aspects for tissue-specific in vivo delivery of CRISPR/Cas9 components using nanomaterials.

Potential Avenues for Exosomal Isolation and Detection Methods to Enhance Small-Cell Lung Cancer Analysis

Around the world, lung cancer has long been the main factor in cancer-related deaths, with small-cell lung cancer (SCLC) being the deadliest form of lung cancer. Cancer cell-derived exosomes and exosomal miRNAs are considered promising biomarkers for diagnosing and prognosis of various diseases, including SCLC. Due to the rapidity of SCLC metastasis, early detection and diagnosis can offer better diagnosis and prognosis and therefore increase the patient's chances of survival. Over the past several years, many methodologies have been developed for analyzing non-SCLC-derived exosomes. However, minimal advances have been made in SCLC-derived exosome analysis methodologies. This Review discusses the epidemiology and prominent biomarkers of SCLC. Followed by a discussion about the effective strategies for isolating and detecting SCLC-derived exosomes and exosomal miRNA, highlighting the critical challenges and limitations of current methodologies. Finally, an overview is provided detailing future perspectives for exosome-based SCLC research.

Technological aspects of manufacturing and analytical control of biological nanoparticles

Extracellular vesicles (EVs) are cell-derived biological nanoparticles that gained great interest for drug delivery. EVs have numerous advantages compared to synthetic nanoparticles, such as ideal biocompatibility, safety, ability to cross biological barriers and surface modification via genetic or chemical methods. On the other hand, the translation and the study of these carriers resulted difficult, mostly because of significant issues in up-scaling, synthesis and impractical methods of quality control. However, current manufacturing advances enable EV packaging with any therapeutic cargo, including DNA, RNA (for RNA vaccines and RNA therapeutics), proteins, peptides, RNA-protein complexes (including gene-editing complexes) and small molecules drugs. To date, an array of new and upgraded technologies have been introduced, substantially improving EV production, isolation, characterization and standardization. The used-to-be "gold standards" of EV manufacturing are now outdated, and the state-of-art requires extensive revision. This review re-evaluates the pipeline for EV industrial production and provides a critical overview of the modern technologies required for their synthesis and characterization.

Sensitive analysis of miRNAs via primer exchange reaction integrated with hairpin catalytic reaction

MicroRNAs (miRNAs) can serve as potential biological targets for early screening, targeted therapy, and prognosis in ovarian cancer (OC). However, sensitive and reliable quantification and identification of miRNA remain a huge challenge. Herein, we proposed a simple and reliable approach for the ultra-sensitive detection of miRNA by integrating endonuclease-III (Exo-III) assisted signal recycle, primer exchange reaction (PER), and hairpin catalytic reaction (HCR). In this method, target miRNA specifically binds with toehold sequence to form a blunt 3' terminus in the detection probe (dumbbell probe) that can be recognized by Exo-III, and to initiate subsequent signal amplifications. Based on this, the approach is successfully utilized in detecting OC related miRNAs with high sensitivity (limit of detection for miRNA-211 was 13 aM) and stability. By simply changing the toehold sequence in detection probe, the established approach can be easily extended to other miRNA detection. We believe that the platform is robust in detecting OS related biomarkers and is promising in renovating cancer diagnostic tools.

One-pot RPA-Cas12a assay for instant and visual detection of Burkholderia pseudomallei

Burkholderia pseudomallei is the causative agent of melioidosis, a potentially life-threatening infectious disease, and poses public health risks in endemic areas. Due to the high mortality, intrinsic antibiotic resistance, and atypical manifestations, establishing a rapid, accurate, and sensitive identification of B. pseudomallei enables earlier diagnosis, proper treatments, and better outcomes of melioidosis. Herein, we present a One-Pot CRISPR-integrated assay for Instant and Visual Detection (termed OPC-IVD) of B. pseudomallei. The integration of recombinase polymerase amplification and CRISPR-Cas12a recognition-activated trans-cleavage, achieved a true all-in-one single-tube reaction system, initiating the amplification and cleavage simultaneously, which realized a facile sample-to-answer assay. This approach could be performed with simplified DNA extraction and completed around 30 min by holding the reaction tube in the hand. The detection limit of our OPC-IVD was determined to be 2.19 copy/uL of plasmid DNA, 12.5 CFU/mL of B. pseudomallei, and 61.5 CFU/mL of bacteria in spiked blood samples, respectively. Furthermore, the introduction of internal amplification control effectively reduced the occurrence of false negatives, which was incorporated in the reaction system, and amplified simultaneously with the target and read by naked eyes. The assay exhibited 100% accuracy when evaluated in clinical isolates and samples. The streamlined workflow of our OPC-IVD of B. pseudomallei enables a field-deployable, instrument-free, and ultra-fast approach that can be utilized by non-expert personnel in the field of molecular diagnosis of melioidosis especially in under-resourced setting.

CRISPR-Cas12a-assisted elimination of the non-specific signal from non-specific amplification in the Exponential Amplification Reaction

Non-specific amplification is a major problem in nucleic acid amplification resulting in false-positive results, especially for exponential amplification reactions (EXPAR). Although efforts were made to suppress the influence of non-specific amplification, such as chemical blocking of the template's 3'-ends and sequence-independent weakening of template-template interactions, it is still a common problem in many conventional EXPAR reactions. In this study, we propose a novel strategy to eliminate the non-specific signal from non-specific amplification by integrating the CRISPR-Cas12a system into two-templates EXPAR. An EXPAR-Cas12a strategy named EXPCas was developed, where the Cas12a system acted as a filter to filter out non-specific amplificons in EXPAR, suppressing and eliminating the influence of non-specific amplification. As a result, the signal-to-background ratio was improved from 1.3 to 15.4 using this method. With microRNA-21 (miRNA-21) as a target, the detection can be finished in 40 min with a LOD of 103 fM and no non-specific amplification was observed.

Cas12a/blocker DNA-based multiplex nucleic acid detection system for diagnosis of high-risk human papillomavirus infection

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins are an innovative tool in molecular diagnostics owing to their high specificity and modularity for target nucleic acid sequences. However, the sequence-indiscriminate trans-cleavage activity of the Cas protein renders multiplex detection challenging. In this study, we developed a Cas12a-based multiplex detection system by designing blocker DNA complementary to reporter DNA, which enables the simultaneous detection of two genes with a single Cas protein in a single reaction. As a proof of concept, we chose high-risk human papillomavirus (HPV) 16 and 18 as the model targets and incorporated recombinase polymerase amplification (RPA) and transcription reactions to achieve high accuracy and sensitivity. Using the proposed system, we detected the genes of both HPV 16 and 18 down to 1 aM within 80 min under isothermal conditions. We validated the performance of the system in detecting genomic DNA from various cell lines and clinical samples from cervical cancer patients with high specificity. The proposed system facilitated rapid multiplex detection of high-risk HPVs in a single reaction tube with only Cas12a, thus representing a more user-friendly and economical alternative to previous Cas protein-based multiplex detection assays. The proposed system has considerable potential for point-of-care testing and could be expanded to detect various nucleic acid biomarkers.

Recent progress in aptamer and CRISPR-Cas12a based systems for non-nucleic target detection

Efficient and sensitive detection of targets is one of the motivations for constant development and innovation of various biosensors. CRISPR-Cas12a, a new generation of gene editing tools, has shown excellent application potential in biosensor design and construction. By combining with the specific recognition element-aptamer, a single-stranded oligonucleotide obtained by systematic evolution of ligands by exponential enrichment (SELEX) in vitro screening, CRISPR-Cas12a also shows superior performance non-nucleic acid targets detection, such as small molecules, proteins, virus and pathogenic bacteria. However, aptamer and CRISPR-Cas12a (CRISPR-Cas12a/Apt) still face some problems in non-nucleic acid target detection, such as single signal response mode and narrow linear range. The development of diverse CRISPR-Cas12a/Apt biosensors is necessary to meet the needs of various detection environments. In this review, the working principle of CRISPR-Cas12a/Apt was introduced and recent progress in CRISPR-Cas12a/Apt in the application of non-nucleic acid target detection was summarized. Moreover, the requirements of critical parameters such as crRNA sequence, activator sequence, and reaction system in the design of CRISPR-Cas12a/Apt biosensors were discussed, which could provide the reference for the design of efficient and sensitive novel non-nucleic acid target biosensors. In addition, the challenges and prospects of CRISPR-Cas12a/Apt-based biosensor were further presented.

CRISPR/Cas systems for the detection of nucleic acid and non-nucleic acid targets

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems are becoming powerful tools for disease biomarkers detection. Due to the specific recognition, cis-cleavage and nonspecific trans-cleavage capabilities, CRISPR/Cas systems have implemented the detection of nucleic acid targets (DNA and RNA) as well as non-nucleic acid targets (e.g., proteins, exosomes, cells, and small molecules). In this review, we first summarize the principles and characteristics of various CRISPR/Cas systems, including CRISPR/Cas9, Cas12, Cas13 and Cas14 systems. Then, various types of applications of CRISPR/Cas systems used in detecting nucleic and non-nucleic acid targets are introduced emphatically. Finally, the prospects and challenges of their applications in biosensing are discussed.

Progress and bioapplication of CRISPR-based one-step, quantitative and multiplexed infectious disease diagnostics

In Vitro Diagnosis (IVD) technology is able to accurately detect pathogens or biomarkers at an initial stage of disease, which works as an important toolbox for disease diagnosis. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) system, as an emerging IVD method, plays a crucial role in the field of infectious disease detection due to its superior sensitivity and specificity. Recently, an increasing number of scientists have been devoted to improving the performance of CRISPR-based detection and on-site point-of-care testing (POCT) from extraction-free detection, amplification-free, modified Cas/crRNA complexes, quantitative assays, one-pot detection, and multiplexed platform. In this review, we describe the potential roles of these novel approaches and platforms in one-pot methods, quantitative molecular diagnostics as well as multiplexed detection. This review will not only help guide the full use of the CRISPR-Cas tools for quantification, multiplexed detection, POCT and as next-generation diagnostic biosensing platforms but also inspire new ideas, technological advances, and engineering strategies to address real-world challenges like the ongoing COVID-19 pandemic.

Functional DNA sensors integrated with nucleic acid signal amplification strategies for non-nucleic acid targets detection

In addition to carrying and transmitting genetic material, some DNA molecules have specific binding ability or catalytic function. DNA with this special function is collectively referred to as functional DNA (fDNA), such as aptamer, DNAzyme and so on. fDNA has the advantages of simple synthetic process, low cost and low toxicity. It also has high chemical stability, recognition specificity and biocompatibility. In recent years, fDNA biosensors have been widely investigated as signal recognition elements and signal transduction elements for the detection of non-nucleic acid targets. However, the main problem of fDNA sensors is their limited sensitivity to trace targets, especially when the affinity of fDNA to the targets is low. To further improve the sensitivity, various nucleic acid signal amplification strategies (NASAS) are explored to improve the limit of detection of fDNA. In this review, we will introduce four NASAS (hybridization chain reaction, entropy-driven catalysis, rolling circle amplification, CRISPR/Cas system) and the corresponding design principles. The principle and application of these fDNA sensors integrated with signal amplification strategies for detection of non-nucleic acid targets are summarized. Finally, the main challenges and application prospects of NASAS integrated fDNA biosensing system are discussed.

Towards Point of Care CRISPR-Based Diagnostics: From Method to Device

Rapid, accurate, and portable on-site detection is critical in the face of public health emergencies. Infectious disease control and public health emergency policymaking can both be aided by effective and trustworthy point of care tests (POCT). A very promising POCT method appears to be the clustered regularly interspaced short palindromic repeats and associated protein (CRISPR/Cas)-based molecular diagnosis. For on-site detection, CRISPR/Cas-based detection can be combined with multiple signal sensing methods and integrated into smart devices. In this review, sensing methods for CRISPR/Cas-based diagnostics are introduced and the advanced strategies and recent advances in CRISPR/Cas-based POCT are reviewed. Finally, the future perspectives of CRISPR and POCT are summarized and prospected.

Exo-III Enzyme and DNAzyme-Assisted Dual Signal Recycles for Sensitive Analysis of Exosomes by Using Personal Glucose Meter

Exosome plays a crucial role in regulating intercellular communication during atherosclerosis development. However, sensitive and portable exosome detection remains a huge challenge. Herein, a personal glucose meter (PGM)-based exosomes detection approach has been proposed that allows detection of exosomes with a high sensitivity and reproducibility. In this method, a catch probe, which is composed of CD63 aptamer and blocker sequence, is utilized for the specific identification of exosomes. The blocker sequence binds with H probe to initiate the Exo-III-assisted signal recycles to generate numerous DNAzyme sequences. Under the assistance of the substrate, DNAzyme forms its active secondary structure to generate gap site in substrate, releasing a linker to conjugate sucrase to streptavidin magnetic beads (SMBs). After removing unbound sucrase, the SMB-linker-sucrase complex is used to catalyze sucrose to glucose, which can be read by PGMs. Based on this, the method exhibits a wide detection range and a low limit of detection, holding a promising prospect for the analysis of exosomes and screening atherosclerosis.