CRISPR/Cas12a-Assisted Chemiluminescence Sensor for Aflatoxin B1 Detection in Cereal Based on Functional Nucleic Acid and In-Pipet Rolling Circle Amplification

Multiple gRNAs-assisted CRISPR/Cas12a-based portable aptasensor enabling glucometer readout for amplification-free and quantitative detection of malathion

BACKGROUND

The threat of toxic malathion residues to human health has always been a serious food safety issue. The CRISPR/Cas system represents an innovative detection technology for pesticide residues, but its application to malathion detection has not been reported yet. In addition, the multiple-guide RNA (gRNA) powered-CRISPR/Cas biosensor has the advantages of being fast, sensitive and does not require pre-amplification. However, the reported multiple-gRNA CRISPR/Cas-based biosensors are largely only used for the detection of nucleic acid targets, and there are still certain challenges in detecting non-nucleic acid targets.

RESULTS

In this work, a multiplex-gRNA-assisted CRISPR/Cas12a-based portable aptasensor (MgCPA) is developed for amplification-free and quantitative detection of malathion using a glucometer. When target malathion is present in the MgCPA strategy, it specifically binds with aptamer and then activates the trans-cleavage activity of the multiplex-gRNA CRISPR/Cas12a. The activated multiple Cas12a/gRNA complexes cut invertase-HP probes on the electrode surface to obtain glucose signals with glucometer assistance. Under optimal conditions, the developed MgCPA strategy achieves satisfactory portable quantitative and sensitive detection of malathion down to 300 fM (S/N = 3) without pre-amplification. Moreover, the satisfactory selectivity, high reproducibility, and good stability of the proposed strategy are also obtained. Due to its excellent and robust shelf life, our developed MgCPA strategy can be practically applied in detecting malathion in orange, apple, cabbage, and spinach samples.

SIGNIFICANCE

Amplification-free, sensitive, portable quantitative and selective detection of malathion in food samples is achieved by employing our developed MgCPA strategy. This strategy not only opens up a new path for the non-nucleic-acid target detection using amplification-free methods based on multiple-gRNA-assisted CRISPR/Cas12a, but also has broad application prospects in ensuring food safety.

Asymmetric CRISPR-Cas12a powered electrochemical aptasensor for clenbuterol detection based on competitive gRNA mediated cascade signal amplification

The residue of clenbuterol (CLB) in food poses a potential harm to human health. Herein, we presented an electrochemical aptasensor (E-A-CRISPR) based on employing an aptamer as a specific recognition element and asymmetric CRISPR-Cas12a as signal amplifiers for sensitive, and selective detection of CLB. In this E-A-CRISPR system, the target CLB bound to the aptamer and initiated cascade signal amplification through the DNase activity of CRISPR-Cas12a with two competitive gRNAs. Upon amplification, the active Cas12a cleaved the methylene blue-labeled hairpin probe on the electrode, reducing the peak current. Under optimal conditions, the E-A-CRISPR system showed a wide linear range (1 pM-100 nM) and a low detection limit (500 fM). This system could detect CLB in potable water, pig liver, and pork samples, showing significant potential for food safety monitoring. To our knowledge, this study is the first to use a CRISPR-Cas12a powered system for electrochemical sensing of CLB.

On-site detection of OTA and AFB1 based on branched hybridization chain reaction coupled with lateral flow assay

Mycotoxins are widely prevalent in various agricultural commodities, whose excessive consumption can pose significant risks to human health. In this study, we developed a facile mycotoxin detection platform based on branched hybridization chain reaction coupled with lateral flow assay. Ochratoxin A/Aflatoxin B1 bind to aptamers triggering the release of initiators, which leads to bHCR amplification and forms three-dimensional dendritic DNA nanostructures. Using the functionalized quantum dots as a fluorescent label, by leveraging smartphones and handheld ultraviolet lamps, the qualitative and quantitative detection of OTA and AFB1 can be achieved with a significantly enhanced sensitivity level, surpassing that of commercial test strips by 2-3 orders of magnitude. The visual detection limits for OTA and AFB1 were 30 pg/mL and 4 pg/mL, respectively. This approach eliminates the necessity for enzyme catalysis or the preparation and purification of antibodies and/or hapten, thereby reducing testing expenses and streamlining operational procedures. Moreover, substituting aptamer and nucleic acid sequences can effectively expand the scope of detection targets. Consequently, the as-proposed strategy exhibits great potential as a versatile technique, suitable for various analytical scenarios due to its sensitivity, accuracy, simplicity, and portability.

CRISPR/Cas12a with Universal crRNA for Indiscriminate Virus Detection

Viruses, known for causing widespread biological harm and even extinction, pose significant challenges to public health. Virus detection is crucial for accurate disease diagnosis and preventing the spread of infections. Recently, the outstanding analytical performance of CRISPR/Cas biosensors has shown great potential and they have been considered as augmenting methods for reverse-transcription polymerase chain reaction (RT-PCR), which was the gold standard for nucleic acid detection. We herein utilized Cas12a with universal CRISPR RNA (crRNA) for indiscriminate virus detection by attaching the target to a longer track strand for isothermal amplification. The amplified products contain a domain that is recognized by the Cas12a/crRNA complex, triggering the cleavage of surrounding reporters to produce signals, thereby escaping the target dependence of crRNA recognition. The proposed method allows the same crRNA to detect multiple viral nucleic acids with high sensitivity, including but not limited to SARS-CoV-2, human papillomaviruses (HPV), HCOV-NL63, HCOV-HKU1, and miRNA biomarkers. Taking SARS-CoV-2 and HPV16 pseudoviruses as examples, this method was proved as a versatile and sensitive platform for molecular diagnostic applications.

Magnetic relaxation switching immunosensor based on polystyrene microcolumn and tyramine signal amplification for ultrasensitive and user-friendly detection of aflatoxin B1 in corn

Aflatoxin B1 is highly mutagenic in humans, and long-term exposure can impair immunity and increase the risk of cancer. It is imperative to develop immunoassays with convenient operation and high sensitivity to detect aflatoxin B1. This study presents a polystyrene microcolumn-mediated magnetic relaxation switching immunosensor based on a tyramine signal amplification strategy for detecting aflatoxin B1. An environmentally friendly hand-held polystyrene microcolumn was designed as an effective immunoreaction carrier, remaining 91% efficiency after 12 repeated uses. And the microcolumn provides a user-friendly procedure for rapid separation and reagent switching within 3 s by simple stirring in solution. The combination of a strong anti-interference magnetic relaxation switching biosensing and an efficient tyramine signal amplification enables the quantitative detection of aflatoxin B1 in the range of 0.01-10 ng/mL, with a limit of detection of 0.006 ng/mL. This method has potential application in the rapid detection of trace food contaminants.

Highly Sensitive One-Pot Isothermal Assay Combining Rolling Circle Amplification and CRISPR/Cas12a for Aflatoxin B1 Detection

Occurrences of mycotoxins in cereals are widespread throughout the world. However, the lack of efficient and ultrasensitive tests has largely impeded the identification of these substances in actual samples. Herein, a novel one-pot isothermal assay that integrates rolling-circle amplification (RCA) and CRISPR/Cas12a to detect aflatoxin B1 (AFB1) is reported. Upon addition of AFB1 to the magnetic bead functionalized with a duplex of the AFB1 aptamer and its complementary DNA (cDNA), the specific recognition of AFB1 by the aptamer causes the release of cDNA to activate the RCA reaction. Subsequently, the RCA amplicon initiates both trans-cleavage and cis-cleavage activities of the endonuclease Cas12a. The synergistic coupling of RCA and CRISPR/Cas12a enables exponential amplification of cDNA, which further promotes CRISPR/Cas12a to nonspecifically cleave the single-stranded DNA reporters with enhanced detection signals. Remarkably, the CRISPR/Cas12a-assisted one-pot isothermal assay can not only achieve ultrasensitive quantitative detection through fluorescence detection, but also achieve visual detection through a lateral flow strip, which improves accessibility to mycotoxin detection in resource-limited regions. The limit of detection was 0.016 and 0.408 ng/mL, respectively. The proposed assay successfully applies in real samples with satisfactory recoveries from 90 to 114%. This study presents a powerful and versatile method for reliable and ultrasensitive detection of mycotoxins in various applications.

Electrochemical Sensors in the Food Sector: A Review

In a world that is becoming increasingly concerned with health, safety, and the sustainability of food supply chains, the control and assurance of food quality have become of utmost importance. This review examines the application and potential of electrochemical sensors in the dynamic field of food science to meet these expanding demands. The article introduces electrochemical sensors and describes their operational mechanics and the components contributing to their function. A summary of the most prevalent electrochemical methods outlines the diverse food analysis techniques available. The review shifts to discussing the food science applications of these sensors, highlighting their crucial role in detecting compounds in food samples like meat, fish, juice, and milk for contemporary quality control. This paper showcases electrochemical sensors' utility in food analysis, underscoring their significance as powerful, efficient tools for maintaining food safety and how they could transform our approach to global food quality control and assurance.

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.

Sensitive and on-Site Detection of Staphylococcus aureus Based on CRISPR/Cas 13a-Assisted Chemiluminescence Resonance Energy Transfer

Developing a specific, sensitive, rapid, and on-site method for detecting pathogenic bacteria in food samples is critical to ensuring public safety. This article demonstrates a CRISPR/Cas13a system and a chemiluminescence resonance energy transfer (CRET) (CRISPR/Cas 13a-assisted CRET)-based strategy for sensitive and on-site detection of pathogenic bacteria in real samples. Once the hybrid double strand of aptamerS. aureus-cRNA recognizes the target model bacteria of Staphylococcus aureus (S. aureus), the released cRNA would bind with CRISPR/Cas 13a to form a complex of cRNA-CRISPR/Cas 13a, which could cleave the RNA molecule in the detecting probe of horseradish peroxidase (HRP) modified-gold nanoparticles (AuNPs) linked by RNA (AuNPs-RNA-HRP), resulting in an enhanced chemiluminescence signal due to the CRET "OFF" phenomenon after introducing the chemiluminescence substrate of luminol. The CRISPR/Cas 13a-assisted CRET strategy successfully detected S. aureus in drinking water and milk with detection limits of 20 and 30 cfu/mL, respectively, within the recovery of 90.07-105.50%. Furthermore, after integrating with an immunochromatographic test strip (ICTS), the CRISPR/Cas 13a-assisted CRET strategy achieved the on-site detection of as low as 102 cfu/mL of S. aureus in drinking water and milk via a smartphone, which is about 10 times lower than that in the previously reported AuNPs-based colorimetric ICTS, demonstrating a convenient and sensitive detection method for S. aureus in real samples.

Electrochemical/photoelectrochemical dual-mode aptasensor for sensitive aflatoxin B1 assay based on distance-modulation strategy using Au NPs/PCZIF-8-ZnO as sensing substrate

Aflatoxin B1 (AFB1), a hepatotoxic and carcinogenic food contaminant, is commonly found in agricultural food. Herein, Au NPs anchored ZIF-8-derived porous carbon-ZnO (Au NPs/PCZIF-8-ZnO) was firstly synthesized to act as the sensing substrate. Then, a ratiometric electrochemical (EC) and "off-on" photoelectrochemical (PEC) dual-mode paper-based aptasensor was presented for AFB1 detection based on a distance-modulation sensing strategy. The independent signal transduction mechanisms and output mode not only broaden the dynamic detection range but also provide a self-verification to assay results, improving the sensitivity and reliability. The wide detection ranges of 0.1 pg/mL-100 ng/mL (EC mode) and 0.02 pg/mL-100 ng/mL (PEC mode) were obtained using dual-mode aptasensor, with detection limits of 36.7 and 9.3 fg/mL, respectively. The fabricated aptasensor exhibited excellent selectivity, reproducibility and stability. Furthermore, it exhibited good practicability for AFB1 assays in real samples, demonstrating great potential applications for food safety evaluation.

Recent advances in nucleic acid signal amplification-based aptasensors for sensing mycotoxins

Mycotoxin contamination in food products may cause serious health hazards and economic losses. The effective control and accurate detection of mycotoxins have become a global concern. Even though a variety of methods have been developed for mycotoxin detection, most conventional methods suffer from complicated operation procedures, low sensitivity, high cost, and long assay time. Therefore, the development of simple and sensitive methods for mycotoxin assay is highly needed. The introduction of nucleic acid signal amplification technology (NASAT) into aptasensors significantly improves the sensitivity and facilitates the detection of mycotoxins. Herein, we give a comprehensive review of the recent advances in NASAT-based aptasensors for assaying mycotoxins and summarize the principles, features, and applications of NASAT-based aptasensors. Moreover, we highlight the challenges and prospects in the field, including the simultaneous detection of multiple mycotoxins and the development of portable devices for field detection.

Isothermal Reciprocal Catalytic DNA Circuit for Sensitive Analysis of Kanamycin

Inappropriate use of veterinary drugs can result in the presence of antibiotic residues in animal-derived foods, which is a threat to human health. A simple yet efficient antibiotic-sensing method is highly desirable. Programmable DNA amplification circuits have supplemented robust toolkits for food contaminants monitoring. However, they currently face limitations in terms of their intricate design and low signal gain. Herein, we have engineered a robust reciprocal catalytic DNA (RCD) circuit for highly efficient bioanalysis. The trigger initiates the cascade hybridization reaction (CHR) to yield plenty of repeated initiators for activating the rolling circle amplification (RCA) circuit. Then the RCA-generated numerous reconstituted triggers can reversely stimulate the CHR circuit. This results in a self-sufficient supply of numerous initiators and triggers for the successive cross-invasion of CHR and RCA amplifiers, thus leading to exponential signal amplification for the highly efficient detection of analytes. With its flexible programmability and modular features, the RCD amplifier can serve as a universal toolbox for the high-performance and accurate sensing of kanamycin in buffer and food samples including milk, honey, and fish, highlighting its enormous promise for low-abundance contaminant analysis in foodstuffs.

An Electrochemical Immunosensor Based on Chitosan-Graphene Nanosheets for Aflatoxin B1 Detection in Corn

We reported a highly efficient electrochemical immunosensor utilizing chitosan-graphene nanosheets (CS-GNs) nanocomposites for the detection of aflatoxin B1 (AFB1) in corn samples. The CS-GNs nanocomposites, serving as a modifying layer, provide a significant specific surface area and biocompatibility, thereby enhancing both the electron transfer rate and the efficiency of antibody immobilization. The electrochemical characterization was conducted utilizing both differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). Moreover, the antibody concentration, pH, antibody immobilization time, and immunoreaction time, were optimized. The results showed that the current change (ΔI) before and after the immunoreaction demonstrated a strong linear relationship (R2=0.990) with the AFB1 concentration, as well as good specificity and stability. The linear range extended from 0.05 to 25 ng/mL, with a detection limit of 0.021 ng/mL (S/N=3). The immunosensor exhibited a recovery rate ranging from 97.3% to 101.4% in corn samples, showing a promising performance using an efficient method, and indicating a remarkable prospect for the detection of fungal toxins in grains.

Rapid and sensitive point-of-need aflatoxin B1 testing in feedstuffs using a smartphone-powered mobile microfluidic lab-on-fiber device

Rapid, high-frequency, and accurate identification of aflatoxin B1 (AFB1) is crucial for ensuring food safety and reducing population mortality. Herein, we constructed Smartphone powered Mobile mIcrofluidic Lab-on-fiber dEvice (SMILE) comprising a compact optical system, fiber nano-bioprobe-embedded microfluidic-chip system, mini-photodetector, and software application to facilitate the rapid and sensitive point-of-need quantitative testing for AFB1. The elegant optical design of SMILE significantly improves light transmission efficiency, detection sensitivity, and portability by integrating a compacted all-fiber optical structure with a fiber nano-bioprobe-embedded microfluidic chip. Furthermore, the nanopore layer of the fiber nano-bioprobe improves detection sensitivity by increasing the biorecognition molecule number and enhancing the interaction between the evanescent field and dye. Through an indirect competitive immunoassay mechanism, SMILE achieves sensitive quantitative detection of AFB1 with a detection limit of 0.08 µg/L. Herein, SMILE was validated using several feedstuff samples tested with a simple aqueous extraction protocol, demonstrating good correlation with high-performance liquid chromatography for AFB1-contaminated feedstuffs. The immunoassay process is completed within 12 min, boasting high sensitivity, specificity, reusability, and reproducibility. Owing to its sensitivity, portability, flexibility, plug-and-play, and smartphone integration, SMILE is highly scalable for rapid and high-frequency point-of-need testing for AFB1 and other trace contaminants.

Space-Confined Electrochemical Aptasensing with Conductive Hydrogels for Enhanced Applicability to Aflatoxin B1 Detection

Aflatoxin B1 (AFB1) contamination has received considerable attention for the serious harm it causes and its wide distribution. Hence, its efficient monitoring is of great importance. Herein, a space-confined electrochemical aptasensor for AFB1 detection is developed using a conductive hydrogel. Plasmonic gold nanoparticles (AuNPs) and methylene blue-embedded double-stranded DNA (MB-dsDNA) were integrated into the conductive Au-hydrogel by ultraviolet (UV) polymerization. Specific recognition of AFB1 by the aptamer released MB from MB-dsDNA in the matrix. The free DNA migrated to the outer layer due to electrostatic repulsion during the Au-hydrogel formation. The electrochemical aptasensor based on this Au-hydrogel offered a twofold enlarged oxidation current of MB (IMB) compared with that recorded in the homogeneous solution for AFB1 detection. Upon light illumination, this IMB was further enlarged by the local surface plasmon resonance (LSPR) of the AuNPs. Ultimately, the Au-hydrogel-based electrochemical aptasensor provided a detection limit of 0.0008 ng mL-1 and a linear range of 0.001-1000 ng mL-1 under illumination for AFB1 detection. The Au-hydrogel allowed for space-confined aptasensing, favorable conductivity, and LSPR enhancement for better sensitivity. It significantly enhanced the applicability of the electrochemical aptasensor by avoiding complicated electrode fabrication and signal loss in a bulk homogeneous solution.

Rapid and sensitive point-of-care PTS-CRISPR assay for food safety monitoring of aflatoxin B1

Food safety is crucial for human health, but its effective on-site monitoring remains a challenge. Pregnancy test strip (PTS) is the successful point-of-care testing (POCT) product of the highest market share in the world, with the cost as low as $0.10 per test. Herein, combined with the CRISPR (clustered regularly interspaced short palindromic repeats) system, PTS-CRISPR was for the first time introduced into food safety monitoring, for rapid and sensitive POCT of aflatoxin B1. The low-cost, easy-to-operate PTS-CRISPR is expected to bring security to the grassroots food market.