A CRISPR/Cas12a-Mediated Dual-Mode Electrochemical Biosensor for Polymerase Chain Reaction-Free Detection of Genetically Modified Soybean

Nanomaterials-Integrated CRISPR/Cas Systems: Expanding the Toolbox for Optical Detection

Nanomaterials-integrated CRISPR/Cas systems have rapidly emerged as powerful next-generation platforms for optical biosensing. These integrated platforms harness the precision of CRISPR/Cas-mediated nucleic acid detection while leveraging the unique properties of nanomaterials to achieve enhanced sensitivity and expanded analytical capabilities, thereby broadening their diagnostic potential. By incorporating a diverse range of nanomaterials, these systems effectively expand the analytical toolbox for optical detection, offering adaptable solutions tailored to various diagnostic challenges. This review provides a comprehensive overview of the nanomaterials successfully integrated into CRISPR/Cas-based optical sensing systems. It examines multiple optical detection modalities, including fluorescence, electrochemiluminescence, colorimetry, and surface-enhanced Raman spectroscopy, highlighting how nanomaterials facilitate signal amplification, enable multiplexing, and support the development of point-of-care applications. Additionally, practical applications of these integrated systems in critical fields such as healthcare diagnostics and environmental monitoring are showcased. While these platforms offer considerable advantages, several real-world challenges such as the complexity of assay workflows, environmental impact of nanomaterials, cost, and regulatory hurdles must be addressed before widespread implementation can be achieved. By identifying these critical obstacles and proposing strategic solutions, we aim to pave the way for the continued advancement and adoption of nanomaterial-integrated CRISPR/Cas optical biosensing technologies.

Current Progress and Future Trends of Genomics-Based Techniques for Food Adulteration Identification

Addressing the pervasive issue of food adulteration and fraud driven by economic interests has long presented a complex challenge. Such adulteration not only compromises the safety of the food supply chain and destabilizes the market economy but also poses significant risks to public health. Food adulteration encompasses practices such as substitution, process manipulation, mislabeling, the introduction of undeclared ingredients, and the adulteration of genetically modified foods. Given the diverse range of deceptive methods employed, genomics-based identification techniques have increasingly been utilized for detecting food adulteration. Compared to traditional detection methods, technologies such as polymerase chain reaction (PCR), next-generation sequencing (NGS), high-resolution melt (HRM) analysis, DNA barcoding, and the CRISPR-Cas system have demonstrated efficacy in accurately and sensitively detecting even trace amounts of adulterants. This paper provides an overview of genomics-based approaches for identifying food adulteration, summarizes the latest applications in certification procedures, discusses current limitations, and explores potential future trends, thereby offering new insights to enhance the control of food quality and contributing to the development of more robust regulatory frameworks and food safety policies.

Signal-off based dual-mode sensing platform for ultrasensitive detection of antibiotics in food samples

Development of efficient and accurate detection methods for antibiotics is crucial for ensuring food safety and safeguarding human health. In this study, a dual-mode sensing platform was constructed by integrating photoelectrochemical (PEC) and surface-enhanced Raman scattering (SERS) techniques for the sensitive detection of kanamycin using an aptamer signal conversion strategy which was based on the C3N4/MXene-gold nanoparticles heterojunction. The sensitive dual-mode sensing platform enabled detection of kanamycin, with linear response ranges of 10-3 to 105 nM for PEC with a detection limit (LOD) of 0.53 pM, and 10-2 to 104 nM for SERS with a LOD of 4.8 pM. Notably, this platform exhibited excellent performance for kanamycin assays in raw milk. Furthermore, combined with various aptamer-targets, it can be easily broadened to detect more low concentration target substances in other complex matrix, showcasing its vast potential for diverse applications.

Recent development of gold nanochips in biosensing and biodiagnosis sensibilization strategies in vitro based on SPR, SERS and FRET optical properties

Gold nanomaterials have become attractive nanomaterials for biomedical research due to their unique physical and chemical properties, and nanochips are designed to manufacture high-quality substrates for loading gold nanoparticles (GNPs) to achieve specific and selective detection. By utilizing multiple optical properties of different gold nanostructures, the sensitivity, specificity, speed, contrast, resolution, and other performance of biosensing and biological diagnosis can be significantly improved. This paper summarized the sensitivity enhancement strategies of optical biosensing techniques based on the three main optical properties of gold nanomaterials: surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS) and fluorescence resonance energy transfer (FRET). The aim is to comprehensively review the development direction of in vitro diagnostics (IVDs) from two aspects: detection strategies and modification of gold nanomaterials. In addition, some opportunities and challenges that gold-based IVDs may encounter at present or in the future are also mentioned in this paper. In summary, this paper can enlighten readers with feasible strategies for manufacturing potential gold-based nanobiosensors.

Multifunctional Ethyl Violet@NH2-MIL-88B(Fe) Hybrids: CRISPR-Cas12a-Assisted PEC-FL-CL Triple-Mode Sensitive Detection of HPV-16

The multimode assay based on multiple response mechanisms has received great attention to effectively improve the accuracy of a sensing platform. However, multifunctional sensing materials for simultaneously satisfying the multiple-mode detections are still in shortage due to the incompatibility of the signal transduction mechanisms in different modes. Here, taking human papillomavirus 16 (HPV-16) DNA (TDNA) as the model due to its important role in cervical cancer, a novel multifunctional material, ethyl violet (EV)@NH2-MIL-88B(Fe) (ENM) hybrids, have been successfully prepared, which could simultaneously satisfy CRISPR-Cas12a-assisted photoelectrochemical (PEC)-fluorescent (FL)-colorimetric (CL) triple-mode detection of TDNA. Based on the TDNA-induced trans-cleavage ability of CRISPR-Cas12a and efficient separation of magnetic beads, ENM was obtained from the single-stranded DNA-surrounded streptavidin-modified magnetic beads-ENM (SMB-ssDNA-ENM) and decomposed by pyrophosphate to get free EV, 2-aminoterephthalic acid (NH2-BDC), and Fe3+. Thus, TDNA was sensitively detected based on the EV-enhanced PEC signal of SnS2 nanosheets (PEC mode), fluorescent signal of NH2-BDC (FL mode), and characteristic absorption peak at about 720 nm of Fe3+-induced Prussian blue (PB) (CL mode). The designed PEC-FL-CL triple-mode biosensing platform had good performance for the detection of TDNA with a wide linear range (0.1 fM-100 nM) and ultralow detection limits (0.07 fM for PEC, 0.03 fM for FL and 0.09 fM for CL). Additionally, the developed PEC-FL-CL triple-mode biosensing platform has great potential for applications in early disease diagnosis and bioanalysis, as it can be easily extended to other DNA assays through modification of the crRNA sequence within the CRISPR-Cas12a system.

Rapid, portable, and sensitive detection of CaMV35S by RPA-CRISPR/Cas12a-G4 colorimetric assays with high accuracy deep learning object recognition and classification

Fast, sensitive, and portable detection of genetic modification contributes to agricultural security and food safety. Here, we developed RPA-CRISPR/Cas12a-G-quadruplex colorimetric assays that can combine with intelligent recognition by deep learning algorithms to achieve sensitive, rapid, and portable detection of the CaMV35S promoter. When the crRNA-Cas12a complex recognizes the RPA amplification product, Cas12 cleaves the G-quadruplex, causing the G4-Hemin complex to lose its peroxide mimetic enzyme function and be unable to catalyze the conversion of ABTS2- to ABTS, allowing CaMV35S concentration to be determined based on ABTS absorbance. By utilizing the RPA-CRISPR/Cas12a-G4 assay, we achieved a CaMV35S limit of detection down to 10 aM and a 0.01 % genetic modification sample in 45 min. Deep learning algorithms are designed for highly accurate classification of color results. Yolov5 objective finding and Resnet classification algorithms have been trained to identify trace (0.01 %) CaMV35S more accurately than naked eye colorimetry. We also coupled deep learning algorithms with a smartphone app to achieve portable and rapid photo identification. Overall, our findings enable low cost ($0.43), high accuracy, and intelligent detection of the CaMV35S promoter.

The type V effectors for CRISPR/Cas-mediated genome engineering in plants

A plethora of CRISPR effectors, such as Cas3, Cas9, and Cas12a, are commonly employed as gene editing tools. Among these, Cas12 effectors developed based on Class II type V proteins exhibit distinct characteristics compared to Class II type VI and type II effectors, such as their ability to generate non-allelic DNA double-strand breaks, their compact structures, and the presence of a single RuvC-like nuclease domain. Capitalizing on these advantages, Cas12 family proteins have been increasingly explored and utilized in recent years. However, the characteristics and applications of different subfamilies within the type V protein family have not been systematically summarized. In this review, we focus on the characteristics of type V effector (CRISPR/Cas12) proteins and the current methods used to discover new effector proteins. We also summarize recent modifications based on engineering of type V effectors. In addition, we introduce the applications of type V effectors for gene editing in animals and plants, including the development of base editors, tools for regulating gene expression, methods for gene targeting, and biosensors. We emphasize the prospects for development and application of CRISPR/Cas12 effectors with the goal of better utilizing toolkits based on this protein family for crop improvement and enhanced agricultural production.

DNA nanoassembly based turn-on amplification probe for sensitive colorimetric CRISPR/Cas12a-mediated detection of pathogen DNA

Clustered regularly interspaced short palindromic repeat (CRISPR) system has been explored as an efficient tool for nucleic acid diagnostics. However, it normally needs instrumentation or produces turn-off signals. Herein, a bulged Y-shape DNA (Y-DNA) nanoassembly was designed and synthesized as a novel turn-on probe. A CRISPR/Cas12a and Y-DNA probe mediated colorimetric assay (named as CYMCOA) strategy was developed for visual detection of pathogen DNA. Upon activating Cas12a with pathogen DNA, the Y-DNA bulge is catalytically trans-cleaved, releasing the G-quadruplex sequence embedded in the Y-DNA nanoassembly as a peroxidase-like DNAzyme. Visible signals with chromogen substrates are thus produced. The CYMCOA strategy was combined with recombinase polymerase amplification (RPA), an isothermal amplification technique, in detecting Helicobacter pylori (Hp) bacteria and SARS-CoV-2 N plasmids as two model pathogens. The bioassay has very excellent detection sensitivity and specificity, owing to the triple cascade amplification reactions and the very low mismatch tolerance. The lower limit of detection values were 0.16 cfu⋅mL-1, 1.5 copies⋅μL-1, and 0.17 copies⋅μL-1 for Hp bacteria, Hp plasmids, and SARS-CoV-2 N plasmids respectively. The detection is fast and accurate. The colorimetric bioassay strategy provides to be a simple, accurate, fast and instrumentation-free platform for nucleic acids detections in various settings, including crude and emergent situations.

A novel dual-model photoelectrochemical/electrochemical sensor based on Z-scheme TiO2 disks/methylene blue for kanamycin detection

Herein, a new dual-model photoelectrochemical (PEC)/electrochemical (EC) sensor based on Z-scheme titanium dioxide (TiO2) disk/methylene blue (MB) sensibilization for the detection of kanamycin (Kana) was developed. Metal-organic framework-derived porous TiO2 disks were synthesized and exhibited excellent anodic photocurrent under visible light excitation. Subsequently, amino-labeled double-stranded DNA (dsDNA) was introduced into the modified electrode. Photocurrent was enhanced with MB embedded in dsDNA to form Z-scheme TiO2/MB sensibilization. When the target, Kana, was present, it specifically bound to the aptamer in the dsDNA, leading to the disruption of the dsDNA structure and the release of MB. This release of MB and the increase in target spatial resistance resulted in a significant weakening of PEC signal and a decreased oxidation peak current of MB. The PEC sensor successfully detected Kana in the range of 2-1000 pM with an LOD of 0.17 pM. Meanwhile, the EC sensor for Kana detection showed a linear range of 5-500 pM with an LOD of 1.8 pM. Additionally, the sensor exhibited excellent selectivity, reproducibility, stability, and good recoveries when applied to milk and honey samples. As a result, this method has the potential for application in ensuring food safety through the rapid determination of antibiotics in food.

CRISPR/Cas-based colorimetric biosensors: a promising tool for the diagnosis of bacterial foodborne pathogens in food products

Some physical phenomena and various chemical substances newly introduced in nanotechnology have allowed scientists to develop valuable devices in the field of food sciences. Regarding such progress, the identification of foodborne pathogenic microorganisms is an imperative subject nowadays. These bacterial species have been found to cause severe health impacts after food ingestion and can result in high mortality in acute cases. The rapid detection of foodborne bacterial species at low concentrations is in high demand in recent diagnostics. CRISPR/Cas-mediated biosensors possess the potential to overcome several challenges in classical assays such as complex pretreatments, long turnaround time, and insensitivity. Among them, colorimetric nanoprobes based on the CRISPR strategy afford promising devices for POCT (point-of-care testing) since they can be visualized with the naked eye and do not require diagnostic apparatus. In this study, we briefly classify and discuss the working principles of the different CRISPR/Cas protein agents that have been employed in biosensors so far. We assess the current status of the CRISPR system, specifically focusing on colorimetric biosensing platforms. We discuss the utilization of each Cas effector in the detection of foodborne pathogens and examine the restrictions of the existing technology. The challenges and future opportunities are also indicated and addressed.

PCR Independent Strategy-Based Biosensors for RNA Detection

RNA is an important information and functional molecule. It can respond to the regulation of life processes and is also a key molecule in gene expression and regulation. Therefore, RNA detection technology has been widely used in many fields, especially in disease diagnosis, medical research, genetic engineering and other fields. However, the current RT-qPCR for RNA detection is complex, costly and requires the support of professional technicians, resulting in it not having great potential for rapid application in the field. PCR-free techniques are the most attractive alternative. They are a low-cost, simple operation method and do not require the support of large instruments, providing a new concept for the development of new RNA detection methods. This article reviews current PCR-free methods, overviews reported RNA biosensors based on electrochemistry, SPR, microfluidics, nanomaterials and CRISPR, and discusses their challenges and future research prospects in RNA detection.

CRISPR/Cas12a-mediated entropy-driven electrochemical biosensor for detection of genetically modified maize Mon810

Genetically modified crops (GMOs) have led to significant, if not revolutionary, agricultural advances. The development of GMOs requires necessary regulations, which depend on the detection of GMOs. A sensitive and specific biosensor for the detection of transgenic crops is crucial to improve the detection efficiency of GMOs. Here, we developed a CRISPR/Cas12a-mediated entropy-driven electrochemiluminescence (ECL) biosensor for the sensitive and specific detection of MON810, the world's most widely used transgenic insect-resistant maize. We designed two crRNAs to activate CRISPR/Cas12a, allowing it to cut non-specific single strands, and we modified the DNA tetrahedron (DT) on the surface of the gold electrode to diminish non-specific adsorption. The entropy-driven chain displacement reaction with the target DNA takes place for amplification. After optimization, the biosensor has satisfactory accuracy and selectivity, with a linear range of ECL of 1-106 fM and a limit of detection (LOD) of 3.3 fM by the 3σ method. The biosensor does not require polymerase chain reaction (PCR) amplification or complex sample processing, which dramatically improves transgenic crop detection efficiency. This new biosensor achieves rapid, sensitive, and highly specific detection of transgenic crops, and has great potential for large-scale field detection of transgenic crops.

A CRISPR/LbCas12a-based method for detection of bacterial fruit blotch pathogens in watermelon

Acidovorax citrulli is the main pathogen causing bacterial fruit blotch, which seriously threatens the global watermelon industry. At present, rapid, sensitive, and low-cost detection methods are urgently needed. The established CRISPR/LbCas12a visual detection method can specifically detect A. citrulli and does not cross-react with other pathogenic bacteria such as Erwinia tracheiphila, Pseudomonas syringae, and Xanthomonas campestris. The sensitivity of this method for genomic DNA detection is as low as 0.7 copies/μL, which is higher than conventional PCR and real-time PCR. In addition, this method only takes 2.5 h from DNA extraction to quantitative detection and does not require complex operation and sample treatment. Additionally, the technique was applied to test real watermelon seed samples for A. citrulli, and the results were contrasted with those of real-time fluorescence quantitative PCR and conventional PCR. The high sensitivity and specificity have broad application prospects in the rapid detection of bacterial fruit blotch bacterial pathogens of watermelon.IMPORTANCEBacterial fruit blotch, Acidovorax citrulli, is an important seed-borne bacterial disease of watermelon, melon, and other cucurbits. The lack of rapid, sensitive, and reliable pathogen detection methods has hampered research on fruit spot disease prevention and control. Here, we demonstrate the CRISPR/Cas12a system to analyze aspects of the specificity and sensitivity of A. citrulli and to test actual watermelon seed samples. The results showed that the CRISPR/Cas12a-based free-amplification method for detecting bacterial fruit blotch pathogens of watermelons was specific for A. citrulli target genes and 100-fold more sensitive than conventional PCR with quantitative real-time PCR. This method provides a new technical tool for the detection of A. citrulli.

Recent progress on the CRISPR/Cas system in optical biosensors

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein systems are adaptive immune systems unique to archaea and bacteria, with the characteristics of targeted recognition and gene editing to resist the invasion of foreign nucleic acids. Biosensors combined with the CRISPR/Cas system and optical detection technology have attracted much attention in medical diagnoses, food safety, agricultural progress, and environmental monitoring owing to their good sensitivity, high selectivity, and fast detection efficiency. In this review, we introduce the mechanism of CRISPR/Cas systems and developments in this area, followed by summarizing recent progress on CRISPR/Cas system-based optical biosensors combined with colorimetric, fluorescence, electrochemiluminescence and surface-enhanced Raman scattering optical techniques in various fields. Finally, we discuss the challenges and future perspectives of CRISPR/Cas systems in optical biosensors.

An LF-NMR homogeneous immunoassay for Vibrio parahaemolyticus based on superparamagnetic 2D nanomaterials

In this work, a sensitive low field nuclear magnetic resonance (LF-NMR) homogeneous immunoassay, also called magnetic resonance switch (MRSw) sensor, for Vibrio parahaemolyticus (VP) was developed. Superparamagnetic 2D nanomaterial was designed and used as the magnetic probe of MRSw sensor. It was GO@SPIONs&Ab, a composite nanomaterial with many superparamagnetic Fe3O4 nanoparticles (SPIONs) providing a magnetic signal and VP antibody (Ab) specifically recognizing the target VP evenly distributed on the surface of GO. The presence of VP controllably changed the aggregation state of the probe, eliminating the uncertainty of MRSw sensor type, and thus then achieving a regular variation of transverse relaxation time T2 and ensuing quantitative detection of VP. Triple signal enhancement of the MRSw sensor was obtained due to the application of the designed 2D probe, by increasing the number of SPIONs, improving the magnetic intensity and susceptibility, and forming a synergistic effect. Under optimized experimental conditions, VP could be detected with satisfied sensitivity, selectivity, precision, accuracy, and stability, even in turbid real samples. LOQ for VP was 10 CFU/mL. This detection principle is widely applicable, providing an idea for the construction of highly sensitive MRSw sensors.

CRISPR/Cas-Powered Amplification-Free Detection of Nucleic Acids: Current State of the Art, Challenges, and Futuristic Perspectives

CRISPR/Cas system is becoming an increasingly influential technology that has been repositioned in nucleic acid detection. A preamplification step is usually required to improve the sensitivity of CRISPR/Cas-based detection. The striking biological features of CRISPR/Cas, including programmability, high sensitivity and sequence specificity, and single-base resolution. More strikingly, the target-activated trans-cleavage could act as a biocatalytic signal transductor and amplifier, thereby empowering it to potentially perform nucleic acid detection without a preamplification step. The reports of such work are on the rise, which is not only scientifically significant but also promising for futuristic end-user applications. This review started with the introduction of the detection methods of nucleic acids and the CRISPR/Cas-based diagnostics (CRISPR-Dx). Next, we objectively discussed the pros and cons of preamplification steps for CRISPR-Dx. We then illustrated and highlighted the recently developed strategies for CRISPR/Cas-powered amplification-free detection that can be realized through the uses of ultralocalized reactors, cascade reactions, ultrasensitive detection systems, or others. Lastly, the challenges and futuristic perspectives were proposed. It can be expected that this work not only makes the researchers better understand the current strategies for this emerging field, but also provides insight for designing novel CRISPR-Dx without a preamplification step to win practicable use in the near future.

DNA Extraction- and Amplification-Free Nucleic Acid Biosensor for the Detection of Foodborne Pathogens Based on CRISPR/Cas12a and Argonaute Protein-Mediated Cascade Signal Amplification

A novel method for detecting low levels of viable foodborne pathogens, specifically Salmonella typhimurium (S. typhimurium), has been developed. Traditional nucleic acid assay, such as polymerase chain reaction (PCR), often requires complex DNA extraction and amplification, making it challenging to differentiate between viable and nonviable pathogens. This assay employed a phage as the recognition element to precisely identify and lyse viable S. typhimurium that can undergo DNA extraction. It combined the efficient trans-cleavage activities of CRISPR/Cas12a with the specific cleavage advantages of Argonaute proteins, enabling ultrasensitive detection. This double-enzyme-mediated nucleic acid test can accurately distinguish viable and nonviable S. typhimurium with a detection limit of 23 CFU/mL without DNA amplification. The method was successfully applied to common food samples, producing results consistent with quantitative PCR tests. This work provides a promising platform for easily detecting viable foodborne pathogens with high sensitivity without the need for DNA extraction and amplification.

CRISPR/Cas System: The Accelerator for the Development of Non-nucleic Acid Target Detection in Food Safety

Non-nucleic acid targets have posed a serious challenge to food safety. The detection of non-nucleic acid targets can enable us to monitor food contamination in a timely manner. In recent years, the CRISPR/Cas system has been extensively explored in biosensing. However, there is a lack of a summary of CRISPR/Cas-powered detection tailored to non-nucleic acid targets involved in food safety. This review comprehensively summarizes the recent advances on the construction of CRISPR/Cas-powered detection and the promising applications in the field of food safety related non-nucleic acid targets. The current challenges and futuristic perspectives are also proposed accordingly. The rapidly evolving CRISPR/Cas system has provided a powerful propellant for non-nucleic acid target detection via integration with aptamer and/or DNAzyme. Compared with traditional analytical methods, CRISPR/Cas-powered detection is conceptually novel, essentially eliminates the dependence on large instruments, and also demonstrates the capability for rapid, accurate, sensitive, and on-site testing.

A one-tube dual-readout biosensor for detection of nucleic acids and non-nucleic acids using CRISPR-ALP tandem assay

Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have been considered a next-generation molecular diagnosis tool. Single-readout mode has been extensively employed in massive CRISPR/Cas12a-based biosensors. In this work, we propose a one-tube dual-readout biosensor (CRISAT) for the first time for the detection of ultrasensitive nucleic acids and non-nucleic acids developed by harnessing CRISPR-ALP tandem assay. In the presence of a target, Cas12a is activated to randomly cut the single-stranded hyDNA sequence of MB@hyDNA-cALP, thus releasing abundant alkaline phosphatase (ALP) in the supernatant solution. By using 4-aminophenol phosphate as the substrate of ALP, p-aminophenol is produced, which then reacts with N-[3-(trimethoxysilyl)propyl]ethylenediamine or diethylenetriamine to generate silicon-containing polymer carbon dots (Si PCDs) or polymer carbon dots (PCDs) in situ, which can be observed by the naked eye or detected using a fluorescent device in the same solution. Using this strategy, a fluorescence and colorimetry dual-readout nanoplatform for CRISPR-based biosensors can be rationally developed. We ascertain the applicability of CRISAT by detecting the SARS-CoV-2 pseudovirus, achieving superior sensitivity and specificity. With simple modification of crRNAs, the CRISAT platform can also be employed to detect monkeypox virus (MPXV) and non-nucleic acids of adenosine triphosphate (ATP). This work shows great potential for the detection of nucleic acids and non-nucleic acids.

CRISPR/Cas12a-Powered EC/FL Dual-Mode Controlled-Release Homogeneous Biosensor for Ultrasensitive and Cross-Validated Detection of Messenger Ribonucleic Acid

Accurate detection of cancer-associated mRNAs is beneficial to early diagnosis and potential treatment of cancer. Herein, for the first time, we developed a novel CRISPR/Cas12a-powered electrochemical/fluorescent (EC/FL) dual-mode controlled-release homogeneous biosensor for mRNA detection. A functionalized ssDNA P2-capped Fe3O4-NH2 loaded with methylene blue (P2@MB-Fe3O4-NH2) was synthesized as the signal probe, while survivin mRNA was chosen as the target RNA. In the presence of the target mRNA, the nicking endonuclease-mediated rolling circle amplification (NEM-RCA) was triggered to produce significant amounts of ssDNA, activating the collateral activity of Cas12a toward the surrounding single-stranded DNA. Thus, the ssDNA P1 completely complementary to ssDNA P2 was cleaved, resulting in that the ssDNA P2 bio-gate on Fe3O4-NH2 could not be opened due to electrostatic interactions. As a result, there was no or only a little MB in the supernatant after magnetic separation, and the measured EC/FL signal was exceedingly weak. On the contrary, the ssDNA P2 bio-gate was opened, enabling MB to be released into the supernatant, and generating an obvious EC/FL signal. Benefiting from the accuracy of EC/FL dual-mode cross-verification, high amplification efficiency, high specificity of NEM-RCA and CRISPR/Cas12a, and high loading of mesoporous Fe3O4-NH2 on signal molecules, the strategy shows aM-level sensitivity and single-base mismatch specificity. More importantly, the practical applicability of this dual-mode strategy was confirmed by mRNA quantification in complex serum environments and tumor cell lysates, providing a new way for developing a powerful disease diagnosis tool.

CRISPR/Cas-Based Diagnostics in Agricultural Applications

Pests and disease-causing pathogens frequently impede agricultural production. An early and efficient diagnostic tool is crucial for effective disease management. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein (Cas) have recently been harnessed to develop diagnostic tools. The CRISPR/Cas system, composed of the Cas endonuclease and guide RNA, enables precise identification and cleavage of the target nucleic acids. The inherent sensitivity, high specificity, and rapid assay time of the CRISPR/Cas system make it an effective alternative for diagnosing plant pathogens and identifying genetically modified crops. Furthermore, its potential for multiplexing and suitability for point-of-care testing at the field level provide advantages over traditional diagnostic systems such as RT-PCR, LAMP, and NGS. In this review, we discuss the recent developments in CRISPR/Cas based diagnostics and their implications in various agricultural applications. We have also emphasized the major challenges with possible solutions and provided insights into future perspectives and potential applications of the CRISPR/Cas system in agriculture.

Flexible carbon fiber cloth supports decorated with cerium metal- organic frameworks and multi-walled carbon nanotubes for simultaneous on-site detection of Cd2+ and Pb2+ in food and water samples

The widespread heavy metal pollution endangers human health; hence, accurate on-site detection and quantification of heavy metal content in the surroundings is a vital step in reversing the harmful effect. Herein, an electrochemical sensor based on flexible cerium metal-organic framework@multi-walled carbon nanotubes/carbon cloth (CeMOF@MWCNTs/CC) was constructed for simultaneous on-site detection of Cd²⁺ and Pb²⁺ in food and water samples. The rich carboxyl groups of MWCNTs provided abundant sites for the adsorption of Cd²⁺ and Pb²⁺, and the mutual conversion of Ce³⁺ and Ce⁴⁺ in CeMOF facilitated the reduction and reoxidation of metal ions. The prepared electrode showed excellent performance in the simultaneous measurement of Cd²⁺ and Pb²⁺, with detection limits of 2.2 ppb and 0.64 ppb, respectively. More importantly, the sensing platform has been successfully used to detect simultaneously Cd²⁺ and Pb²⁺ in grain and water samples, and the detection results were consistent with the standard methods, showing great potential in environmental monitoring and food safety.

Recent Advances in Electrochemical Biosensors for Food Control

The rapid and sensitive detection of food contaminants is becoming increasingly important for timely prevention and treatment of foodborne disease. In this review, we discuss recent developments of electrochemical biosensors as facile, rapid, sensitive, and user-friendly analytical devices and their applications in food safety analysis, owing to the analytical characteristics of electrochemical detection and to advances in the design and production of bioreceptors (antibodies, DNA, aptamers, peptides, molecular imprinted polymers, enzymes, bacteriophages, etc.). They can offer a low limit of detection required for food contaminants such as allergens, pesticides, antibiotic traces, toxins, bacteria, etc. We provide an overview of a broad range of electrochemical biosensing designs and consider future opportunities for this technology in food control.

Multifunctional Photoelectrochemical Biosensor Based on ZnIn2S4/ZnS QDs@Au-Ag-Reversed Photocurrent of Cu-Metal-Organic Framework Coupled with CRISPR/Cas-12a-Shearing for Assay of Dual Targets

False positives and negatives in bioanalytical assays remain a persistent problem. Herein, a multifunctional photoelectrochemical (PEC) biosensor based on ZnIn₂S₄ (ZIS)/ZnS quantum dots (QDs)@Au-Ag-reversed photocurrent of Cu-metal-organic framework (MOF) coupled with CRISPR/Cas-12a-shearing was innovatively developed for assay of dual targets. First, Cu-MOF as a good PEC material shows cathodic photocurrent. Then, numerous ZIS/ZnS QDs were assembled to the Au-Ag nanoparticles (NPs) to prepare a stable and highly amplified signal probe, which can just match the energy level of Cu-MOFs and realized the polarity-reversed photocurrent of Cu-MOF for the first time. As the empty-core nanostructure of Au-Ag NPs has a high specific surface area and low material density, the bimetallic nanocrystal can much increase the reaction rate and improve the redox efficiency. When target CEA-produced cDNA opened the hairpin DNA (HP1 DNA) on the electrode, the ZIS/ZnS QDs@Au-Ag signal probe was conjugated to the electrode via DNA hybridization, achieving a significantly reversed PEC current for CEA detection. Moreover, the specific binding of kanamycin/aptamer generated the acDNA (activator), which can activate the trans-cleavage activity of the CRISPR-CAS12a system on ssDNA, so the signal probe was sheared and caused the obvious decrease of PEC signal for kanamycin detection. The newly developed ZIS/ZnS QDs@Au-Ag NPs displayed excellent PEC properties and reversed photocurrent to MOF and were combined with the unique CRISPR-Cas12a system to achieve sensitive detection of dual targets, which can open a new polarity-reversed PEC sensing platform for rapid and accurate analysis of multiple targets and can effectively avoid false positives results in clinical testing.

An Ultrasensitive Colorimetric Foodborne Pathogenic Detection Method Using a CRISPR/Cas12a Mediated Strand Displacement/Hybridization Chain Reaction

Accurate, rapid, and sensitive pathogenic detections play an important role in food safety. Herein, we developed a novel CRISPR/Cas12a mediated strand displacement/hybridization chain reaction (CSDHCR) nucleic acid assay for foodborne pathogenic colorimetric detection. A biotinylated DNA toehold is coupled on avidin magnetic beads and acts as an initiator strand to trigger the SDHCR. The SDHCR amplification allowed the formation of long hemin/G-quadruplex-based DNAzyme products to catalyze the TMB-H₂O₂ reaction. In the presence of the DNA targets, the trans-cleavage activity of CRISPR/Cas12a was activated to cleave the initiator DNA, resulting in the failure of SDHCR and no color change. Under optimal conditions, the CSDHCR has a satisfactory linear detection of DNA targets with a regression equation Y = 0.0531*X - 0.0091 (R² = 0.9903) in the range of 10 fM to 1 nM, and the limit of detection was determined as 4.54 fM. In addition, Vibrio vulnificus, one foodborne pathogen, was used to verify the practical application of the method, and it showed satisfactory specificity and sensitivity with a limit of detection at 1.0 × 10⁰ CFU/mL coupling with recombinase polymerase amplification. Our proposed CSDHCR biosensor could be a promising alternative method for ultrasensitive and visual detection of nucleic acids and the practical application of foodborne pathogens.

Electrochemical sensor for single-cell determination of bacteria based on target-triggered click chemistry and fast scan voltammetry

Herein, an electrochemical sensor for single-cell determination of bacteria was developed based on target-triggered click chemistry and fast scan voltammetry (FSV). In it, bacteria not only are the detection target, but also can use their own metabolism to achieve first-level signal amplification. More electrochemical labels were immobilized on functionalized 2D nanomaterials to achieve second-level signal amplification. At 400 V/s, FSV can achieve third-level signal amplification. The linear range and limit of quantification (LOQ) are 1 ∼ 10⁸ CFU/mL and 1 CFU/mL, respectively. When the reaction time of E. coli-instructed Cu²⁺ reduction is extended to 120 min, PCR-free single-cell determination of E. coli was achieved by electrochemical method first time. The feasibility of the sensor was verified by analysis of E. coli in seawater and milk samples with recoveries ranging from 94% to 110%. This detection principle is widely applicable, providing a new path for the establishment of single-cell detection strategy for bacteria.

Review of CRISPR/Cas Systems on Detection of Nucleotide Sequences

Nowadays, with the rapid development of biotechnology, the CRISPR/Cas technology in particular has produced many new traits and products. Therefore, rapid and high-resolution detection methods for biotechnology products are urgently needed, which is extremely important for safety regulation. Recently, in addition to being gene editing tools, CRISPR/Cas systems have also been used in detection of various targets. CRISPR/Cas systems can be successfully used to detect nucleic acids, proteins, metal ions and others in combination with a variety of technologies, with great application prospects in the future. However, there are still some challenges need to be addressed. In this review, we will list some detection methods of genetically modified (GM) crops, gene-edited crops and single-nucleotide polymorphisms (SNPs) based on CRISPR/Cas systems, hoping to bring some inspiration or ideas to readers.

Amplification-free CRISPR/Cas detection technology: challenges, strategies, and perspectives

Rapid and accurate molecular diagnosis is a prerequisite for precision medicine, food safety, and environmental monitoring. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)-based detection, as a cutting-edged technique, has become an immensely effective tool for molecular diagnosis because of its outstanding advantages including attomolar level sensitivity, sequence-targeted single-base specificity, and rapid turnover time. However, the CRISPR/Cas-based detection methods typically require a pre-amplification step to elevate the concentration of the analyte, which may produce non-specific amplicons, prolong the detection time, and raise the risk of carryover contamination. Hence, various strategies for target amplification-free CRISPR/Cas-based detection have been developed, aiming to minimize the sensitivity loss due to lack of pre-amplification, enable detection for non-nucleic acid targets, and facilitate integration in portable devices. In this review, the current status and challenges of target amplification-free CRISPR/Cas-based detection are first summarized, followed by highlighting the four main strategies to promote the performance of target amplification-free CRISPR/Cas-based technology. Furthermore, we discuss future perspectives that will contribute to developing more efficient amplification-free CRISPR/Cas detection systems.

Electrochemiluminescence biosensor for DNA adenine methylation methyltransferase based on CRISPR/Cas12a trans-cleavage-induced dual signal enhancement

In this work, an electrochemiluminescence (ECL) biosensor with dual signal enhancement was constructed and used for DNA adenine methylation methyltransferase (Dam MTase) detection. At present of Dam MTase, restriction endonuclease (DPnI) cleaves hairpin DNA (HP) and releases the HP stem end as a single strand that can activate CRISPR/Cas12a trans-cleavage activity. Assisted by trans-cleavage, the distance between the signal quenching factor ferrocene (Fc) and the ECL signal unit increased, and the repulsion between the signal unit and the Indium Tin Oxides (ITO) electrode decreased. The above results resulted in an enhanced ECL signal. ECL intensity has a good linear relationship with the logarithm of Dam MTase concentration in the range of 5-70 U/mL with a detection limit of 23.4 mU/mL. The proposed biosensor was successfully utilized to detect of Dam MTase in serum samples.

Overview on the Design of Magnetically Assisted Electrochemical Biosensors

Electrochemical biosensors generally require the immobilization of recognition elements or capture probes on the electrode surface. This may limit their practical applications due to the complex operation procedure and low repeatability and stability. Magnetically assisted biosensors show remarkable advantages in separation and pre-concentration of targets from complex biological samples. More importantly, magnetically assisted sensing systems show high throughput since the magnetic materials can be produced and preserved on a large scale. In this work, we summarized the design of electrochemical biosensors involving magnetic materials as the platforms for recognition reaction and target conversion. The recognition reactions usually include antigen-antibody, DNA hybridization, and aptamer-target interactions. By conjugating an electroactive probe to biomolecules attached to magnetic materials, the complexes can be accumulated near to an electrode surface with the aid of external magnet field, producing an easily measurable redox current. The redox current can be further enhanced by enzymes, nanomaterials, DNA assemblies, and thermal-cycle or isothermal amplification. In magnetically assisted assays, the magnetic substrates are removed by a magnet after the target conversion, and the signal can be monitored through stimuli-response release of signal reporters, enzymatic production of electroactive species, or target-induced generation of messenger DNA.

Dual-mode photoelectrochemical/electrochemical sensor based on Z-scheme AgBr/AgI-Ag-CNTs and aptamer structure switch for the determination of kanamycin

A "signal-on" dual-mode aptasensor based on photoelectrochemical (PEC) and electrochemical (EC) signals was established for kanamycin (Kana) assay by using a novel Z-scheme AgBr/AgI-Ag-CNTs composite as sensing platform, an aptamer structure switch, and K₃[Fe(CN)₆] as photoelectron acceptor and electrochemical signal indicator. The aptamer structure switch was designed to obtain a "signal-off" state, which included an extended Kana aptamer (APT), one immobilized probe (P1), and one blocking probe (P2) covalently linked with graphdiyne oxide (GDYO) nanosheets. P1, P2, and aptamer formed the double helix structure, which resulted in the inhibited photocurrent intensity because of the weak conductivity of double helix layer and serious electrostatic repulsion of GDYO towards K₃[Fe(CN)₆]. In the presence of Kana, APT specifically bound to the target and dissociated from P1 and P2, and thus, a "signal-on" state was initiated by releasing P2-GDYO from the platform. Based on the sensing platform and the aptamer structure switch, the dual-mode aptasensor realized the linear determination ranges of 1.0 pM-2.0 μM with a detection limit (LOD) of 0.4 pM (for PEC method) and 10 pM-5.0 μM with a LOD of 5 pM (for EC method). The aptasensor displayed good application potential for Kana test in real samples.

Electrochemiluminescence covalent organic framework coupling with CRISPR/Cas12a-mediated biosensor for pesticide residue detection

The trace detection of pesticide residue becomes particularly important since increasing attentions have been attached to food safety. Herein, we developed an electrochemiluminescence (ECL) covalent organic framework (COF) based-biosensor for trace pesticide detection coupling with CRISPR/Cas12a-mediated signal accumulation strategy. Firstly, the target conversion was carried out with an aptamer-assembled magnetic spherical nucleic acids, which can convert acetamiprid to activator DNA, triggering the CRISPR/Cas12a to make quenching probes far away from electrode for signal accumulation. The COF with stable and strong ECL was synthesized by a condensation reaction between the perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) and melamine (MA), due to the highly ordered arrangement of the PTCDA luminescence units among COF structure and the pore confinement effect. Moreover, the designed assay method was successfully employed to detect the residual level of acetamiprid in real sample and expected to be widely used in pesticide-related food safety.

Nucleic acid isothermal amplification-based soft nanoarchitectonics as an emerging electrochemical biosensing platform

The emergence of nucleic acid isothermal amplification strategies based on soft nanoarchitectonics offers a new dimension to the traditional electrochemical technique, particularly because of its flexibility, high efficiency, and increased sensitivity for analytical applications. Various DNA/RNA isothermal amplification strategies have been developed for the design and fabrication of new electrochemical biosensors for efficient and important biomolecular detection. Herein, we provide an overview of recent efforts in this research field and the strategies for signal-amplified sensing systems, with their biological applications, current challenges and prospects in this promising new area.

CRISPR/Cas12a-Triggered Chemiluminescence Enhancement Biosensor for Sensitive Detection of Nucleic Acids by Introducing a Tyramide Signal Amplification Strategy

CRISPR-based biosensors have attracted increasing attention in accurate and sensitive nucleic acid detection. In this work, we report a CRISPR/Cas12a-triggered chemiluminescence enhancement biosensor for the ultrasensitive detection of nucleic acids by introducing tyramide signal amplification for the first time (termed CRICED). The hybrid chain DNA (crDNA) formed by NH₂-capture DNA (capDNA) and biotin-recognition DNA (recDNA) was preferentially attached to the magnetic beads (MBs), and the streptavidin-HRP was subsequently introduced to obtain MB@HRP-crDNA. In the presence of the DNA target, the activated CRISPR/Cas12a is capable of randomly cutting initiator DNA (intDNA) into vast short products, and thus the fractured intDNA could not trigger the toehold-mediated DNA-strand displacement reaction (TSDR) event with MB@HRP-crDNA. After the addition of tyramine-AP and H₂O₂, abundant HRP-tyramine-AP emerges through the covalent attachment of HRP-tyramine, exhibiting enhanced chemiluminescence (CL) signals or visual image readouts. By virtue of this biosensor, we achieved high sensitivity of synthetic DNA target and amplified DNA plasmid using recombinase polymerase amplification (RPA) as low as 17 pM and single-copy detection, respectively. Our proposed CRICED was further evaluated to test 20 HPV clinical samples, showing a superior sensitivity of 87.50% and specificity of 100.00%. Consequently, the CRICED platform could be an attractive means for ultrasensitive and imaging detection of nucleic acids and holds a promising strategy for the practical application of CRISPR-based diagnostics.

Advances in Electrochemical Techniques for the Detection and Analysis of Genetically Modified Organisms: An Analysis Based on Bibliometrics

Since the first successful transgenic plants obtained in 1983, dozens of plants have been tested. On the one hand, genetically modified plants solve the problems of agricultural production. However, due to exogenous genes of transgenic plants, such as its seeds or pollen drift, diffusion between populations will likely lead to superweeds or affect the original traits. The detection technology of transgenic plants and their products have received considerable attention. Electrochemical sensing technology is a fast, low-cost, and portable analysis technology. This review interprets the application of electrochemical technology in the analysis and detection of transgenic products through bibliometrics. A total of 83 research articles were analyzed, spanning 2001 to 2021. We described the different stages in the development history of the subject and the contributions of countries and institutions to the topic. Although there were more annual publications in some years, there was no explosive growth in any period. The lack of breakthroughs in this technology is a significant factor in the lack of experts from other fields cross-examining the subject. Through keyword co-occurrence analysis, different research directions on this topic were discussed. The use of nanomaterials with excellent electrical conductivity allows for more sensitive detection of GM crops by electrochemical sensors. Furthermore, co-citation analysis was used to interpret the most popular reports on the topic. In the end, we predict the future development of this topic according to the analysis results.