CRISPR/Cas12a-mediated liposome-amplified strategy for the photoelectrochemical detection of nucleic acid

Cascade branch migration-triggered strand displacement amplification for specific and sensitive detection of microRNA

MicroRNAs (miRNAs) have been involved in many biological processes and are regarded as promising biomarkers. The short sequence, low abundance and highly homologous interference sequences greatly hinder the accurate detection of miRNAs. Here, a cascade branch migration-triggered strand displacement amplification (CBM-TSDA) strategy was developed for the first time for specific and sensitive detection of miRNA-155 (miR-155). In the presence of target miR-155, the CBM was initiated and two Y-shaped probes were eventually produced. Next, the Y-shaped probes were transformed into three-way junction (3WJ) structures and triggered the SDA to produce a large number of G-quadruplex (G4) structures. Finally, the increased fluorescence signal of G4/Thioflavin T (ThT) was used to quantify miR-155. Meanwhile, the colorimetric responses of the G4-hemin DNAzyme could be used as supplementary detection to obtain a dual-mode signal readout. This detection strategy showed high detection sensitivity, and the limit of detection was 0.28 pM in the fluorescence detection mode and 0.34 pM in the colorimetric detection mode. Notably, it showed high detection specificity, being able to discriminate the single-base mutations of the target with a high discrimination factor. The strategy also possessed excellent capacity for miR-155 detection in cell lysates and real human blood samples. The developed strategy provides a promising detection platform for miRNA, which may be applied to early clinical diagnosis.

Sensitive, Semiquantitative, and Portable Nucleic Acid Detection of Rabies Virus Using a Personal Glucose Meter

Rabies is a zoonotic infection with the potential to infect all mammals and poses a significant threat to mortality. Although enzyme-linked immunosorbent tests and real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) have been established for rabies virus (RABV) detection, they require skilled staff. Here, we introduce a personal glucose meter (PGM)-based nucleic acid (NA-PGM) detection method to diagnose RABV. This method ensures sensitive and convenient RABV diagnosis through hybridization of reverse transcription-recombinase aided amplification (RT-RAA) amplicons with probes labeled with sucrose-converting enzymes, reaching a detection level as low as 6.3 copies/μL equivalent to 12.26 copies. NA-PGM allows for the differentiation of RABV from other closely related viruses. In addition, NA-PGM showed excellent performance on 65 clinical samples with a 100% accuracy rate compared with the widely adopted RT-qPCR method. Thus, our developed NA-PGM method stands out as sensitive, semiquantitative, and portable for RABV detection, showcasing promise as a versatile platform for a wide range of pathogens.

A new strategy based on a cascade amplification strategy biosensor for on-site eDNA detection and outbreak warning of crown-of-thorns starfish

Population outbreaks of the crown-of-thorns starfish (COTS) seriously threaten the sustainability of coral reef ecosystems. However, traditional ecological monitoring techniques cannot provide early warning before the outbreaks, thus preventing timely intervention. Therefore, there is an urgent need for a more accurate and faster technology to predict the outbreaks of COTS. In this work, we developed an electrochemical biosensor based on a programmed catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) cyclic amplification strategy for sensitive and selective detection of COTS environmental DNA (eDNA) in water bodies. This biosensor exhibited excellent electrochemical characteristics, including a low limit of detection (LOD = 18.4 fM), low limit of quantification (LOQ = 41.1 fM), and wide linear range (50 fM - 10 nM). The biosensing technology successfully allowed the detection of COTS eDNA in the aquarium environment, and the results also demonstrated a significant correlation between eDNA concentration and COTS number (r = 0.990; P < 0.001). The reliability and accuracy of the biosensor results have been further validated through comparison with digital droplet PCR (ddPCR). Moreover, the applicability and accuracy of the biosensor were reconfirmed in field tests at the COTS outbreak site in the South China Sea, which has shown potential application in dynamically monitoring the larvae before the COTS outbreak. Therefore, this efficient electrochemical biosensing technology offers a new solution for on-site monitoring and early warning of the COTS outbreak.

Split activator of CRISPR/Cas12a for direct and sensitive detection of microRNA

CRISPR/Cas12a-based nucleic acid assays have been increasingly used for molecular diagnostics. However, most current CRISPR/Cas12a-based RNA assays require the conversion of RNA into DNA by preamplification strategies, which increases the complexity of detection. Here, we found certain chimeric DNA-RNA hybrid single strands could activate the trans-cleavage activity of Cas12a, and then discovered the activating effect of split ssDNA and RNA when they are present simultaneously. As proof of concept, split nucleic acid-activated Cas12a (SNA-Cas12a) strategy was developed for direct detection of miR-155. By adding a short ssDNA to the proximal end of the crRNA spacer sequence, we realized the direct detection of RNA targets using Cas12a. With the assistance of ssDNA, we extended the limitation that CRISPR/Cas12a cannot be activated by RNA targets. In addition, by taking advantage of the programmability of crRNA, the length of its binding to DNA and RNA was optimized to achieve the optimal efficiency in activating Cas12a. The SNA-Cas12a method enabled sensitive miR-155 detection at pM level. This method was simple, rapid, and specific. Thus, we proposed a new Cas12a-based RNA detection strategy that expanded the application of CRISPR/Cas12a.

MicroRNA Sensors Based on CRISPR/Cas12a Technologies: Evolution From Indirect to Direct Detection

MicroRNA (miRNA) has emerged as a promising biomarker for disease diagnosis and a potential therapeutic targets for drug development. The detection of miRNA can serve as a noninvasive tool in diseases diagnosis and predicting diseases prognosis. CRISPR/Cas12a system has great potential in nucleic acid detection due to its high sensitivity and specificity, which has been developed to be a versatile tool for nucleic acid-based detection of targets in various fields. However, conversion from RNA to DNA with or without amplification operation is necessary for miRNA detection based on CRISPR/Cas12a system, because dsDNA containing PAM sequence or ssDNA is traditionally considered as the activator of Cas12a. Until recently, direct detection of miRNA by CRISPR/Cas12a system has been reported. In this review, we provide an overview of the evolution of biosensors based on CRISPR/Cas12a for miRNA detection from indirect to direct, which would be beneficial to the development of CRISPR/Cas12a-based sensors with better performance for direct detection of miRNA.

Cas-based bacterial detection: recent advances and perspectives

Persistent bacterial infections pose a formidable threat to global health, contributing to widespread challenges in areas such as food safety, medical hygiene, and animal husbandry. Addressing this peril demands the urgent implementation of swift and highly sensitive detection methodologies suitable for point-of-care testing and large-scale screening. These methodologies play a pivotal role in the identification of pathogenic bacteria, discerning drug-resistant strains, and managing and treating diseases. Fortunately, new technology, the CRISPR/Cas system, has emerged. The clustered regularly interspaced short joint repeats (CRISPR) system, which is part of bacterial adaptive immunity, has already played a huge role in the field of gene editing. It has been employed as a diagnostic tool for virus detection, featuring high sensitivity, specificity, and single-nucleotide resolution. When applied to bacterial detection, it also surpasses expectations. In this review, we summarise recent advances in the detection of bacteria such as Mycobacterium tuberculosis (MTB), methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli (E. coli), Salmonella and Acinetobacter baumannii (A. baumannii) using the CRISPR/Cas system. We emphasize the significance and benefits of this methodology, showcasing the capability of diverse effector proteins to swiftly and precisely recognize bacterial pathogens. Furthermore, the CRISPR/Cas system exhibits promise in the identification of antibiotic-resistant strains. Nevertheless, this technology is not without challenges that need to be resolved. For example, CRISPR/Cas systems must overcome natural off-target effects and require high-quality nucleic acid samples to improve sensitivity and specificity. In addition, limited applicability due to the protospacer adjacent motif (PAM) needs to be addressed to increase its versatility. Despite the challenges, we are optimistic about the future of bacterial detection using CRISPR/Cas. We have already highlighted its potential in medical microbiology. As research progresses, this technology will revolutionize the detection of bacterial infections.

CRISPR/Cas detection with nanodevices: moving deeper into liquid biopsy

The emerging field of liquid biopsy has garnered significant interest in precision diagnostics, offering a non-invasive and repetitive method for analyzing bodily fluids to procure real-time diagnostic data. The precision and accuracy offered by the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas) technology have advanced and broadened the applications of liquid biopsy. Significantly, when combined with swiftly advancing nanotechnology, CRISPR/Cas-mediated nanodevices show vast potential in precise liquid biopsy applications. However, persistent challenges are still associated with off-target effects, and the current platforms also constrain the performance of the assays. In this review, we highlight the merits of CRISPR/Cas systems in liquid biopsy, tracing the development of CRISPR/Cas systems and their current applications in disease diagnosis particularly in liquid biopsies. We also outline ongoing efforts to design nanoscale devices with improved sensing and readout capabilities, aiming to enhance the performance of CRISPR/Cas detectors in liquid biopsy. Finally, we identify the critical obstacles hindering the widespread adoption of CRISPR/Cas liquid biopsy and explore potential solutions. This feature article presents a comprehensive overview of CRISPR/Cas-mediated liquid biopsies, emphasizing the progress in integrating nanodevices to improve specificity and sensitivity. It also sheds light on future research directions in employing nanodevices for CRISPR/Cas-based liquid biopsies in the realm of precision medicine.

Genosensor on-chip paper for point of care detection: A review of biomedical analysis and food safety application

Over the last decade, paper-based biosensing has attracted considerable attention in numerous fields due to several advantages of them. To elaborate, using paper as a substrate of sensing approaches can be considered an affordable sensing approach owing to low cost of paper, and alongside that, the ability to operate without requiring external equipment. In many cases, cost-effective fabrication techniques such as screen printed and drop casting can be supposed as other benefits of these platforms. Despite the portability and affordability of paper-based assay, two important limitations including sensitivity and selectivity can decrease the application of these sensing approaches. Initially, decoration of paper substrate with nanomaterials (NMs) can improve the properties of paper due to high surface area and conductivity of them. Secondly, the presence of bioreceptors can provide a selective detection platform. Among different bioreceptors, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) can play a significant role. From this perspective, paper-based biosensors can be used for the detection of various gens which related to biomedical or food safety. In this review, we attempted to summarize recent trends and applications of paper-based genosensor, along with critical arguments in terms of NMs role in signal amplification. Furthermore, the lack of paper-based genosensors in field the of biomedical and food safety will be discussed in the following.

CRISPR/Cas12-based electrochemical biosensors for clinical diagnostic and food monitoring

Each organism has a unique sequence of nitrogenous bases in in the form of DNA or RNA which distinguish them from other organisms. This characteristic makes nucleic acid-based detection extremely selective and compare to other molecular techniques. In recent years, several nucleic acid-based detection technology methods have been developed, one of which is the electrochemical biosensor. Electrochemical biosensors are known to have high sensitivity and accuracy. In addition, the ease of miniaturization of this electrochemical technique has garnered interest from many researchers. On the other hand, the CRISPR/Cas12 method has been widely used in detecting nucleic acids due to its highly selective nature. The CRISPR/Cas12 method is also reported to increase the sensitivity of electrochemical biosensors through the utilization of modified electrodes. The electrodes can be modified according to detection needs so that the biosensor's performance can be improved. This review discusses the application of CRISPR/Cas12-based electrochemical biosensors, as well as various electrode modifications that have been successfully used to improve the performance of these biosensors in the clinical and food monitoring fields.

CRISPR/Cas12a and G-quadruplex DNAzyme-driven multimodal biosensor for visual detection of Aflatoxin B1

Aflatoxin B1 (AFB1) contamination severely threatens human and animal health, it is thus critical to construct a strategy for its rapid, accurate, and visual detection. Herein, a multimodal biosensor was proposed based on CRISPR/Cas12a cleaved G-quadruplex (G4) for AFB1 detection. Briefly, specific binding of AFB1 to the aptamer occupied the binding site of the complementary DNA (cDNA), and cDNA then activated Cas12a to cleave G4 into fragments. Meanwhile, the intact G4-DNAzyme could catalyze 3, 3', 5, 5'-tetramethylbenzidine (TMB) to form colourimetric/SERS/fluorescent signal-enhanced TMBox, and the yellow solution produced by TMBox under acidic conditions could be integrated with a smartphone application for visual detection. The colourimetric/SERS/fluorescent biosensor yielded detection limits of 0.85, 0.79, and 1.65 pg·mL-1, respectively, and was applied for detecting AFB1 in peanut, maize, and badam samples. The method is suitable for visual detection in naturally contaminated peanut samples and has prospective applications in the food industry.

Design strategies and advanced applications of primer exchange reactions in biosensing: A review

Early disease diagnosis relies on the sensitive detection and imaging of biomarkers. Signal amplification is one of the most commonly used methods to improve detection sensitivity. Primer exchange reaction (PER) is a novel signal amplification technique that has garnered attention because of its simple and sensitive features. The classical PER involves a single catalytic hairpin, which enables the attachment of custom sequences to the primer chain, generating a long repeat sequence that can bind numerous signaling molecules and achieve powerful signal amplification. Currently, numerous PER-based signal amplification strategies are available that can improve detection sensitivity and promote the development of the signal amplification field. This review focuses on the mechanism of typical PER, the diversification of PER, and PER-based biosensors for various targets. Finally, the challenges and prospects of PER development are discussed.

Ultrathin mesoporous BiOCl nanosheets-mediated liposomes for photoelectrochemical immunoassay with in-situ signal amplification

Designing new biochemical sensors and achieving selectivity and high-sensitivity analysis is one of main research directions for immunoassays. Herein, a liposome-amplification photoelectrochemical (PEC) immunoassay was developed using ultrathin mesoporous bismuth chloride oxide nanosheets (BiOCl MSCN) for the highly selective and sensitive detection of carcinoembryonic antigen (CEA). Based on good photocurrent response of BiOCl MSCN toward dopamine, a liposome-conjugated secondary antibody loaded with dopamine was added for specific recognition in the presence of CEA. After the lysis treatment, the liberated dopamine was injected into the three-electrode electrolytic cell to enhance the photocurrent of BiOCl MSCN. Under the optimized conditions, the constructed liposome-mediated PEC immunoassay showed high sensitivity against CEA, with a dynamic response in the linear range of 0.05 ng mL-1 to 100 ng mL-1 and a detection limit of 35 pg mL-1. The present study proposes a new approach to the liposome-mediated PEC immunoassay constructed on ultrathin mesoporous BiOCl nanosheets, which can be used to target further the study of the sensing mechanism.

High-entropy effect with hollow (ZnCdFeMnCu)xS nanocubes for photoelectrochemical immunoassay

High entropy (HE) compounds with chemically disordered multi-cation structures have become a hot research topic because of their fascinating "cocktail effect". However, high entropy effect with the efficient photoelectric response has not been reported for photoelectrochemical (PEC) immunoassays. Herein, an innovative PEC immunoassay for the sensitive detection of prostate-specific antigen (PSA) was ingeniously constructed using hollow nanocubic (ZnCdFeMnCu)xS photoactive matrices with high entropic effect via the cation exchange. Initially, a sandwich-type immunoreaction has behaved using dopamine-loaded liposome labeled with anti-PSA secondary antibodies. In the presence of PSA, addition of Triton X-100 caused the liposomal cleavage to release dopamine, which was then detected as a reduced photocurrent on (ZnCdFeMnCu)xS-based photoelectrode. Under optimal condition, the PEC immunoassay showed good photocurrent responses toward target PSA with the dynamic linear range of 0.1-50 ng mL-1 with a limit of detection of 34.1 pg mL-1. Significantly, this system can provide a new platform for the development of PEC immunoassays by coupling with high-entropy photoactive materials.

HCR/DNAzyme-triggered cascaded feedback cycle amplification for self-powered dual-photoelectrode detection of femtomolar HPV16

For high-performance dual-photoelectrode assay, developing a pair of photoactive materials with well-matched band structure and the design of a powerful sensing strategy are highly desirable. Herein, the Zn-TBAPy pyrene-based MOF and BiVO4/Ti3C2 Schottky junction were employed as photocathode and photoanode to form an efficient dual-photoelectrode system. The integration of the cascaded hybridization chain reaction (HCR)/DNAzyme-assisted feedback amplification with DNA walker-mediated cycle amplification strategy realizes femtomolar HPV16 dual-photoelectrode bioassay. Through the activation of the HCR cascaded with the DNAzyme system in the presence of HPV16, plentiful HPV16 analogs are generated that leads to exponential positive feedback signal amplification. Meanwhile on the Zn-TBAPy photocathode, the NDNA hybridizes with the bipedal DNA walker followed by circular cleavage by Nb.BbvCI NEase, producing a dramatically enhanced PEC readout. The achieved ultralow detection limit of 0.57 fM and a wide linear range of 10-6 nM-103 nM showcase the excellent performance of the developed dual-photoelectrode system.

Utility of CRISPR/Cas mediated electrochemical biosensors

Electrochemical biosensors represent a class of sensors that employ biological materials as sensitive elements, electrodes as conversion elements, and potential or current as detection signals. The integration of CRISPR/Cas systems into electrochemical biosensors holds immense potential, offering enhanced versatility, heightened sensitivity and specificity, reduced recovery time, and the ability to capture and identify analytes at low concentrations. In this review, we provided a succinct summary of the fundamental principles underlying electrochemical biosensors and CRISPR/Cas systems, and new progress of electrochemical biosensors based on CRISPR/Cas systems in virus, bacteria, and cancer detections. Besides, we discussed its pros and cons, present gaps, potential problem-solvers, and future prospects. To sum up, CRISPR/Cas mediated electrochemical biosensors will surely benefit us a lot in the detection of cells and microorganisms, and of course in other promising fields.

Universal probe-based SNP genotyping with visual readout: a robust and versatile method

Detection of single nucleotide polymorphisms (SNPs) is critical for personalized clinical diagnosis, treatment, and medication. Current clinical detection methods suffer from primer dimerization and require the redesigning of reaction systems for different targets, resulting in a time-consuming and laborious process. Here, we present a robust and versatile method for SNP typing by using tailed primers and universal small molecule probes in combination with a visualized lateral flow assay (LFA). This approach enables not only rapid typing of different targets, but also eliminates the interference of primer dimers and enhances the accuracy and reliability of the results. Our proposed universal assay has been successfully applied to the typing of four SNP loci of clinical samples to verify the accuracy and universality, and the results are consistent with those obtained by Sanger sequencing. Therefore, our study establishes a new universal "typing formula" using nucleic acid tags and small molecule probes that provides a powerful genotyping platform for genetic analysis and molecular diagnostics.

Inspired by game theory: Multi-signal output photoelectrochemical point-of-care immunoassay based on target-triggered organic electronic barriers

This work presents an integrated photoelectrochemical, impedance and colorimetric biosensing platform for flexible detection of cancer markers based on the targeted response by combining liposome amplification strategies and target-induced non-in situ formation of electronic barriers as the signal transduction modality on carbon-modified CdS photoanodes. Inspired by game theory, the carbon layer modified CdS hyperbranched structure with low impedance and high photocurrent response was firstly obtained by surface modification of CdS nanomaterials. Through a liposome-mediated enzymatic reaction amplification strategy, a large number of organic electron barriers were formed by a biocatalytic precipitation (BCP) reaction triggered by horseradish peroxidase released from cleaved liposomes after the introduction of the target molecule, thereby increasing the impedance characteristics of the photoanode as well as attenuating the photocurrent. The BCP reaction in the microplate was accompanied by a significant color change, which opened up a new window for point-of-care testing. Taking carcinoembryonic antigen (CEA) as a proof of concept, the multi-signal output sensing platform showed a satisfactory sensitive response to CEA with an optimal linear range of 20 pg mL^-1-100 ng mL^-1. The detection limit was as low as 8.4 pg mL^-1. Meanwhile, with the assistance of a portable smartphone and a miniature electrochemical workstation, the electrical signal obtained was synchronized with the colorimetric signal to correct the actual target concentration in the sample, further reducing the occurrence of false reports. Importantly, this protocol provides a new idea for the sensitive detection of cancer markers and the construction of a multi-signal output platform.

Ultrasensitive and Specific Clustered Regularly Interspaced Short Palindromic Repeats Empowered a Plasmonic Fiber Tip System for Amplification-Free Monkeypox Virus Detection and Genotyping

The urgent necessity for highly sensitive diagnostic tools has been accentuated by the ongoing mpox (monkeypox) virus pandemic due to the complexity in identifying asymptomatic and presymptomatic carriers. Traditional polymerase chain reaction-based tests, despite their effectiveness, are hampered by limited specificity, expensive and bulky equipment, labor-intensive operations, and time-consuming procedures. In this study, we present a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a-based diagnostic platform with a surface plasmon resonance-based fiber tip (CRISPR-SPR-FT) biosensor. The compact CRISPR-SPR-FT biosensor, with a 125 μm diameter, offers high stability and portability, enabling exceptional specificity for mpox diagnosis and precise identification of samples with a fatal mutation site (L108F) in the F8L gene. The CRISPR-SPR-FT system can analyze viral double-stranded DNA from mpox virus without amplification in under 1.5 h with a limit of detection below 5 aM in plasmids and about 59.5 copies/μL when in pseudovirus-spiked blood samples. Our CRISPR-SPR-FT biosensor thus offers fast, sensitive, portable, and accurate target nucleic acid sequence detection.

The development of a fluorescence/colorimetric biosensor based on the cleavage activity of CRISPR-Cas12a for the detection of non-nucleic acid targets

Nano-biosensors are of great significance for the analysis and detection of important biological targets. Surprisingly, the CRISPR-Cas12a system not only provides us with excellent gene editing capabilities, it also plays an important role in biosensing due to its high base resolution and high levels of sensitivity. However, most CRISPR-Cas12a-based sensors are limited by their recognition and output modes, are therefore only utilized for the detection of nucleic acids using fluorescence as an output signal. In the present study, we further explored the potential application of CRISPR-Cas12a and developed a CRISPR-Cas12a-based fluorescence/colorimetric biosensor (UCNPs-Cas12a/hydrogel-MOF-Cas12a) that provides an efficient targeting system for small molecules and protein targets. These two sensors yield multiple types of signal outputs by converting the target molecule into a deoxyribonucleic acid (DNA) signal input system using aptamers, amplifying the DNA signal by catalyzed hairpin assembly (CHA), and then combining CRISPR-Cas12a with various nanomaterials. UCNPs-Cas12a/hydrogel-MOF-Cas12a exhibited prominent sensitivity and stability for the detection of estradiol (E2) and prostate-specific antigen (PSA), and was successfully applied for the detection of these targets in milk and serum samples. A major advantage of the hydrogel-MOF-Cas12a system is that the signal output can be observed directly. When combined with aptamers and nanomaterials, CRISPR-Cas12a can be used to target multiple targets, with a diverse array of signal outputs. Our findings create a foundation for the development of CRISPR-Cas12a-based technologies for application in the fields of food safety, environmental monitoring, and clinical diagnosis.

An enzyme-responsive electrochemical DNA biosensor achieving various dynamic range by using only-one immobilization probe

Developing a simple and easy-to-operate biosensor with tunable dynamic range would provide enormous opportunities to promote the diagnostic applications. Herein, an enzyme-responsive electrochemical DNA biosensor is developed by using only-one immobilization probe. The immobilization probe was designed with a two-loop hairpin-like structure that contained the mutually independent target recognition and enzyme (EcoRI restriction endonuclease) responsive domains. The target recognition was based on a toehold-mediated strand displacement reaction strategy. The toehold region was initially caged in the loop of the immobilization probe and showed a relatively low binding affinity with target, which was improved via EcoRI cleavage of immobilization probe to liberate the toehold region. The EcoRI cleavage operation for immobilization probe demonstrated the well regulation ability in detection performance. It showed a largely extended dynamic range, a significantly lowered detection limit and better discrimination ability toward the mismatched sequences whether in two buffers (with high or low salt concentrations) or in the serum system. The advantages also includes simplicity in probe design, and facile biosensor fabrication and operation. It thus opens a new avenue for the development of the modulated DNA biosensor and hold a great potential for the diagnostic applications and drug monitoring.

CRISPR/Cas12a-based MUSCA-PEC strategy for HSV-1 assay

In the photoelectrochemical sensing, constant potential excitation to get the photoelectrochemical signal is the main excitation signal mode. Novel method for photoelectrochemical signal obtaining is needed. Inspired by this ideal, a photoelectrochemical strategy for Herpes simplex virus (HSV-1) detection with multiple potential step chronoamperometry (MUSCA) pattern was fabricated using CRISPR/Cas12a cleavage coupled with entropy-driven target recycling. In the presence of target, HSV-1, the Cas12a was activated by the H₁-H₂ complex obtained by entropy-driven, then digesting the circular fragment of csRNA to expose single-stranded crRNA2 and alkaline phosphatase (ALP). The inactive Cas12a was self-assembled with crRNA2 and activated again with the help of assistant dsDNA. After multiple rounds of CRISPR/Cas12a cleavage and magnetic separation, MUSCA, as a signal amplifier, collected the enhanced photocurrent responses generated by catalyzed p-Aminophenol (p-AP). Different from the reported signal enhancement strategies based on photoactive nanomaterials and sensing mechanisms, MUSCA technique endowed the strategy with unique advantages of direct, fast and ultrasensitive. A superior detection limit of 3 aM toward HSV-1 was achieved. This strategy was successfully applied for HSV-1 detection in Human serum samples. The combination of MUSCA technique and CRISPR/Cas12a assay brings broader potential prospect for the detection of nucleic acids.

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.

CRISPR-Cas system manipulating nanoparticles signal transduction for cancer diagnosis

Early diagnosis of cancer is important to improve the survival rate and relieve patient pain. Sensitive detection of cancer related biomarkers in body fluids is a critical approach for the early diagnosis of cancer. The clustered regularly interspaced short palindromic repeat-associated protein (CRISPR-Cas) system has emerged as a molecular manipulation technology because of its simple detection procedure, high base resolution, and isothermal signal amplification. Recently, various nanomaterials with unique optical and electrical characteristics have been introduced as the novel signal transducers to enhance the detection performance of CRISPR-Cas-based nanosensors. This review summarizes the working mechanisms of the CRISPR-Cas system for biosensing. It also enumerates the strategies of CRISPR-manipulated nanosensors based on various signal models for cancer diagnosis, including colorimetric, fluorescence, electrochemical, electrochemiluminescence, pressure, and other signals. Finally, the prospects and challenges of CRISPR-Cas-based nanosensors for cancer diagnostic are also discussed. This article is categorized under: Diagnostic Tools > Biosensing.

An ultrasensitive electrochemical DNA biosensor for monitoring Human papillomavirus-16 (HPV-16) using graphene oxide/Ag/Au nano-biohybrids

A DNA-based electrochemical biosensor has been developed herein for the detection of Human papillomavirus-16 (HPV-16). HPV-16 is a double-stranded, non-enveloped, epitheliotropic DNA virus which responsible for cervical cancer. In this proposed biosensor, an indium tin oxide (ITO) coated glass electrode was modified for sensing HPV-16 using graphene oxide and silver coated gold nanoparticles. Subsequently, HPV-16 specific DNA probes were immobilized on a modified ITO surface. The synthesized nanocomposites were characterized by FE-SEM and UV-VIS spectroscopy techniques. Electrochemical characterization was performed by using cyclic voltammetry and electrochemical Impedance Spectroscopy methods. The hybridization between the probe and target DNA was analyzed by a reduction in current, mediated by methylene blue. The biosensor showed a qualitative inequity between the probe and target HPV-16 DNA. The developed biosensor showed high sensitivity as 0.54 mA/aM for the detection of HPV-16. In a linear range of 100 aM to 1 μM with 100 aM LOD, the proposed biosensor exhibited excellent performance with the rapid diagnosis. Thus, the results indicate that the developed HPV DNA biosensor shows good consistency with the present approaches and opens new opportunities for developing point-of-care devices. The diagnosis of HPV-16 infection in its early stage may also be possible with this detection system.

Integrated slip valve-assisted fluidic chip coupling with CRISPR/Cas12a system for nucleic acid analysis

Currently, some on-site nucleic acid detection platforms have been developed. However, these platforms still need to be improved in device integration and multiple detection capability. In this work, an integrated dual nucleic acid analysis platform was developed by slip valve-assisted fluidic chip coupled with CRISPR/Cas12a system. All the reagents, including nucleic acid extraction, air-dried loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a detection reagents, were preloaded on the fluidic chip. Liquids transfer and stirring could be controlled by a slip valve and a syringe. By combining duplex LAMP reaction with two CRISPR detection units, CRISPR/Cas12a-based dual nucleic acid analysis was successfully constructed. Benefiting from high-quality nucleic acid extraction on the chip, as low as 30 copies/reaction of Vibrio parahaemolyticus (V. parahaemolyticus) and 20 copies/reaction of Salmonella typhimurium (S. typhimurium) could be simultaneously detected. Detection results could be observed by the naked eye under a portable ultraviolet lamp. The whole detection procedure was finished within 60 min. This method with integrated nucleic acid analysis, dual detection capability and fluorescence visualized results provides a new solution for on-site nucleic acid analysis.

Optically Active Nanomaterials and Its Biosensing Applications-A Review

This article discusses optically active nanomaterials and their optical biosensing applications. In addition to enhancing their sensitivity, these nanomaterials also increase their biocompatibility. For this reason, nanomaterials, particularly those based on their chemical compositions, such as carbon-based nanomaterials, inorganic-based nanomaterials, organic-based nanomaterials, and composite-based nanomaterials for biosensing applications are investigated thoroughly. These nanomaterials are used extensively in the field of fiber optic biosensing to improve response time, detection limit, and nature of specificity. Consequently, this article describes contemporary and application-based research that will be of great use to researchers in the nanomaterial-based optical sensing field. The difficulties encountered during the synthesis, characterization, and application of nanomaterials are also enumerated, and their future prospects are outlined for the reader's benefit.

A Label-Free Photoelectrochemical Biosensor Based on CRISPR/Cas12a System Responsive Deoxyribonucleic Acid Hydrogel and "Click" Chemistry

A novel label-free photoelectrochemical (PEC) biosensor is presented in this work. As a barrier, the DNA hydrogel could block the coupling between g-C₃N₄ and CdS quantum dots (QDs). Therefore, extremely low photocurrent signals were obtained. The presence of target microRNA-21 can initiate the rolling circle amplification (RCA) reaction, which in turn produces many repeated sequences to activate the CRISPR/Cas12a system. The trans-cleavage activity of the CRISPR/Cas12a system led to the degradation of DNA hydrogels efficiently. As a result, the g-C₃N₄/CdS QDs heterojunction was formed through "click" chemistry. Through the amplification of the RCA and CRISPR/Cas12a system, the sensitivity of the PEC biosensor was improved significantly with the detection limit of 3.2 aM. The proposed sensor also showed excellent selectivity and could be used to detect actual samples. In addition, the modular design could facilitate the detection of different objects. Thus, the proposed CRISPR/Cas12a system responsive DNA hydrogel provides a simple, sensitive, and flexible way for label-free PEC analysis.

Cluster-Dominated Electrochemiluminescence of Tertiary Amines in Polyethyleneimine Nanoparticles: Mechanism Insights and Sensing Application

Designing and screening highly efficient and cost-effective luminophores have always been a challenge to develop sensitive electrochemiluminescence (ECL) biosensors. Herein, polyethyleneimine nanoparticles (PEI NPs), a kind of nonconjugated polymer (NCP) NPs with tertiary amine clusters, were developed as an ECL luminophore. Specifically, PEI NPs were synthesized by a one-step hydrothermal method using PEI and formaldehyde. The properties of PEI NPs were investigated in detail using photochemical and electrochemical techniques. The results showed cluster-dominated luminescence of tertiary amines in PEI NPs via "through-space conjugation". This non-negligible ECL performance (at 631 nm) was also verified by the initiated reduction-oxidation process. With persulfate as a coreactant, PEI NPs acted as both the luminophore and coreaction accelerator to enhance the ECL intensity remarkably, which was eightfold higher than that of isolated PEI. Moreover, choosing dopamine as the model target, a highly sensitive "signal off" ternary ECL sensor was constructed utilizing PEI NPs as the luminophore. Dopamine could be oxidized to benzoquinone at the sensing interface, quenching the signal via ECL energy transfer. Free from any signal amplification, the proposed sensor achieved a low detection limit (4.3 nM) for target monitoring with good selectivity and stability. This strategy not only provides a unique perspective for designing novel efficient and facile ECL luminophores of tertiary amines but also broadens the biological application of NCP NPs.

Portable electroanalytical nucleic acid amplification tests using printed circuit boards and open-source electronics

The realization of electrochemical nucleic acid amplification tests (NAATs) at the point of care (POC) is highly desirable, but it remains a challenge given their high cost and lack of true portability/miniaturization. Here we show that mass-produced, industrial standardized, printed circuit boards (PCBs) can be repurposed to act as near-zero cost electrodes for self-assembled monolayer-based DNA biosensing, and further integration with a custom-designed and low-cost portable potentiostat. To show the analytical capability of this system, we developed a NAAT using isothermal recombinase polymerase amplification, bypassing the need of thermal cyclers, followed by an electrochemical readout relying on a sandwich hybridization assay. We used our sensor and device for analytical detection of the toxic microalgae Ostreopsis cf. ovata as a proof of concept. This work shows the potential of PCBs and open-source electronics to be used as powerful POC DNA biosensors at a low-cost.

Photoactivatable CRISPR/Cas12a Strategy for One-Pot DETECTR Molecular Diagnosis

As a golden partner of recombinase polymerase amplification (RPA), CRISPR/Cas12a has been proven to solve the false-positive problem caused by nonspecific amplification perfectly; meanwhile, its trans-cleave activity has further enhanced the sensitivity. However, the solution transfer operation after tube cap opening greatly increases the risk of aerosol contamination of amplicon, which is inconsistent with point-of-care (POC) diagnostics requirements. This study proposes a photoactivated CRISPR/Cas12a strategy to achieve one-pot high-sensitivity nucleic acid detection. Using photocleavable complementary ssDNA to block crRNA, RPA amplification can smoothly pass through the exponential interval without being affected by activated Cas12a in the critical early stage. After enough amplicons were produced, the Cas12a test was activated by short bursts of ultraviolet radiation at 365 nm. This one-pot method achieved a sensitivity of 2.5 copies within 40 min. This simple and sensitive one-pot method can effectively avoid amplicon contamination and lower the threshold for molecular diagnostics in POC.

Current Progress in Aptasensor for Ultra-Low Level Monitoring of Parkinson's Disease Biomarkers

In today's world, Parkinson's disease (PD) has been introduced as a long-term degenerative disorder of the central nervous system which mainly affects approximately more than ten million people worldwide. The vast majority of diagnostic methods for PD have operated based on conventional sensing platforms, while the traditional laboratory tests are not efficient for diagnosis of PD in the early stage due to symptoms of this common neurodegenerative syndrome starting slowly. The advent of the aptasensor has revolutionized the early-stage diagnosis of PD by measuring related biomarkers due to the myriad advantages of originating from aptamers which can be able to sensitive and selective capture various types of related biomarkers. The progress of numerous sensing platforms and methodologies in terms of biosensors based on aptamer application for PD diagnosis has revealed promising results. In this review, we present the latest developments in myriad types of aptasensors for the determination of related PD biomarkers. Working strategies, advantages and limitations of these sensing approaches are also mentioned, followed by prospects and challenges.

Photoelectrochemical bioanalysis of microRNA on yolk-in-shell Au@CdS based on the catalytic hairpin assembly-mediated CRISPR-Cas12a system

This work reports on the proof-of-concept of a photoelectrochemical (PEC) biosensor with a horseradish peroxidase-single stranded DNA-encoded magnetic bead (MB-ssDNA-HRP) signal probe cleaved by the catalytic hairpin assembly (CHA)-mediated clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a system for the quantification of microRNA (miR-21) by using yolk-in-shell Au@CdS as a photoactive material.

Size-Controlled Engineering Photoelectrochemical Biosensor for Human Papillomavirus-16 Based on CRISPR-Cas12a-Induced Disassembly of Z-Scheme Heterojunctions

Photoelectrochemical (PEC) biosensors incorporating biomolecular recognition with photon-to-electron conversion capabilities of the photoactive species have been developed for molecular diagnosis, but most involve difficulty in adjusting band gap positions and are unsuitable for PEC biodetection. In this work, an innovative PEC biosensor combined with quantum size-controlled engineering based on quantum confinement by controlling the quantum size was designed for the detection of human papillomavirus-16 (HPV-16) through CRISPR-Cas12a (Cpf1)-induced disassembly of Z-scheme heterojunction. To the best of our knowledge, quantum size-controlled engineering that precisely tunes the properties of photoactive materials is first utilized in the PEC bioanalysis. Based on the quantum size effect, the light absorption efficiency and charge-transfer rate were tuned to suitable levels to obtain the best PEC performance. After incubation with target HPV-16, the binding of Cas12a-crRNA to the target double-stranded DNA (dsDNA) stimulated the activity of indiscriminate cleavage toward single-stranded DNA (ssDNA), resulting in a decrease in photocurrent due to the blocking of electron transfer through the heterojunction. By optimizing experimental conditions, the Z-scheme sensing system exhibited incredible photocurrent response to HPV-16 in the range from 3.0 pM to 600 nM with a detection limit of 1.0 pM. Impressively, the application of the quantum size effect could stimulate more interest in the precise design of band gap structure to improve PEC performance.

"RESET" Effect: Random Extending Sequences Enhance the Trans-Cleavage Activity of CRISPR/Cas12a

The trans-cleavage activity of CRISPR/Cas12a has been widely used in biosensing applications. However, the lack of exploration on the fundamental properties of CRISPR/Cas12a not only discourages further in-depth studies of the CRISPR/Cas12a system but also limits the design space of CRISPR/Cas12a-based applications. Herein, a "RESET" effect (random extending sequences enhance trans-cleavage activity) is discovered for the activation of CRISPR/Cas12a trans-cleavage activity. That is, a single-stranded DNA, which is too short to work as the activator, can efficiently activate CRISPR/Cas12a after being extended a random sequence from its 3'-end, even when the random sequence folds into secondary structures. The finding of the "RESET" effect enriches the CRISPR/Cas12a-based sensing strategies. Based on this effect, two CRISPR/Cas12a-based biosensors are designed for the sensitive and specific detection of two biologically important enzymes.

6-Aza-2-thio-thymine-gold nanoclusters: an excellent candidate in the photoelectrochemical field

The high performance of the photoelectrochemical (PEC) properties of AuNCs can be achieved with 6-aza-2-thio-thymine-AuNCs (ATT-AuNCs) as a photoactive material. The ATT-AuNCs yielded a cathodic photocurrent density as high as 88 μA cm^-2 with O₂ as electron acceptor, which is three orders of magnitude higher than those of other AuNCs in aqueous solutions. Moreover, ATT-AuNCs also show a higher carrier density, shorter Debye length, and smaller depletion layer width than those of reported AuNCs. This work not only reveals the PEC performance and mechanism of ATT-AuNCs, but also establishes a framework for in-depth design and studying the PEC performance of AuNCs.

CRISPR-Cas12a-Derived Photoelectrochemical Biosensor for Point-Of-Care Diagnosis of Nucleic Acid

This work presented a point-of-care (POC) photoelectrochemical (PEC) biosensing for the detection of human papillomavirus-16 (HPV-16) on a portable electrochemical detection system by using CRISPR-Cas12a trans-cleaving the G-quadruplex for the biorecognition/amplification and a hollow In₂O₃-In₂S₃-modified screen-printed electrode (In₂O₃-In₂S₃/SPE) as the photoactive material. G-quadruplexes were capable of biocatalytic precipitation (H₂O₂-mediated 4-chloro-1-naphthol oxidation) on the In₂O₃-In₂S₃/SPE surface, resulting in a weakened photocurrent, but suffered from trans-cleavage when the CRISPR-Cas12a system specifically recognized the analyte. The photocurrent results could be directly observed with the card-sized electrochemical device via a smartphone, which displayed a high-value photocurrent for these positive samples, while a low-value photocurrent for the target-free samples. Such a system exhibited satisfying photocurrent responses toward HPV-16 within a wide working range from 5.0 to 5000 pM and allowed for detection of HPV-16 at a concentration as low as 1.2 pM. The proposed assay provided a smartphone signal readout to enable the rapid screening PEC determination of HPV-16 concentration without sophisticated instruments, thus meeting the requirements of remote areas and resource-limited settings. We envision that combining an efficient biometric PEC sensing platform with a wireless card-sized electrochemical device will enable high-throughput POC diagnostic analysis.

Development of a Rapid and Efficient RPA-CRISPR/Cas12a Assay for Mycoplasma pneumoniae Detection

Mycoplasma pneumoniae (MP) is a one of most common pathogen in causing respiratory infection in children and adolescents. Rapid and efficient diagnostic methods are crucial for control and treatment of MP infections. Herein, we present an operationally simple, rapid and efficient molecular method for MP identification, which eliminates expensive instruments and specialized personnel. The method combines recombinase polymerase amplification (RPA) with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated proteins (Cas) 12a-based detection, with an optimal procedure less than 1 h from sample to result including DNA extraction (25 min), RPA reaction (39°C for 15-20 min), CRISPR/Cas12a detection (37°C for 10 min) and visual detection by naked eyes (2 min). This diagnostic method shows high sensitivity (two copies per reaction) and no cross-reactivity against other common pathogenic bacteria. Preliminary evaluation using 201 clinical samples shows sensitivity of 99.1% (107/108), specificity of 100% (93/93) and consistency of 99.5% (200/201), compared with real-time PCR method. The above data demonstrate that our developed method is reliable for rapid diagnosis of MP. In conclusion, the RPA-CRISPR/Cas12a has a great potential to be as a useful tool for reliable and quick diagnosis of MP infection, especially in primary hospitals with limited conditions.

DIRECT2: A novel platform for a CRISPR-Cas12-based assay comprising universal DNA-IgG probe and a direct lateral flow test

CRISPR-Cas12-based biosensors are a promising tool for the detection of nucleic acids. After dsDNA-target-activated Cas12 cleaves the ssDNA probe, a lateral flow test (LFT) is applied for rapid, simple, and out-of-laboratory detection of the cleaved probe. However, most of the existing approaches of LFT detection have disadvantages related to inverted test/control zones in which the assay result depends not only on the cleavage of the probe but also on the second factor: the binding of the non-cleaved probe in the control zone. We proposed a novel platform for the detection of trans-cleaved DNA using a universal DNA-IgG probe and LFT with the sequential direct location of test and control zones. The advantage of the platform consists of the assay result depending only on the cleaved probe. For this, we designed a composite probe that comprise two parts: the DNA part (biotinylated dsDNA connected to ssDNA with fluorescein) (FAM), and the antibody part (mouse anti-FAM IgG). The Cas12, with guide RNA, was activated by the dsDNA-target. The activated Cas12 cleaved the probe, releasing the ssDNA-FAM-IgG reporter that was detected by the LFT. The sandwich LFT was proposed with anti-mouse IgG adsorbed in the test zone and on the surface of gold nanoparticles. We called the platform with direct location zones and direct analyte-signal dependence the DNA-Immunoglobulin Reporter Endonuclease Cleavage Test (DIRECT²). Therefore, this proof-of-concept study demonstrated that the combination of the proposed DNA-IgG probe and direct LFT opens new opportunities for CRISPR-Cas12 activity detection and its bioanalytical applications.

Dual-amplified CRISPR-Cas12a bioassay for HIV-related nucleic acids

Nucleic acid amplification strategies have successfully dominated ultrasensitive bioassays, but they sometimes bring high time-consumption, multi-step operation, increased contamination risk, and mismatch-related inaccuracy. We proposed a nucleic acid amplification-free method called the AuNPs-tagging based CRISPR-Cas12a bioassay platform. The signal amplification was realized by integrating the self-amplification effect of CRISPR-Cas12a with the enhancement effect of the large number of detectable atoms inside each gold nanoparticle. The proposed method achieved a low LOD of 1.05 amol in 40 min for HIV-related DNA.

Liposome-Mediated In Situ Formation of Type-I Heterojunction for Amplified Photoelectrochemical Immunoassay

Exploiting innovative sensing mechanisms and their rational implementation for selective and sensitive detection has recently become one of the mainstream research directions of photoelectrochemical (PEC) bioanalysis. In contrast to existing conventional strategies, this study presents a new liposome-mediated method via in situ combining ZnInS nanosheets (ZIS NSs) with SnS₂ to form a ZIS NSs/SnS₂ type-I heterojunction on fluorine-doped tin oxide (FTO) electrodes for highly sensitive PEC immunoassays. Specifically, alkaline phosphatase (ALP)-encapsulated liposomes were confined within 96-well plates by sandwich immunorecognition and subsequently subjected to lysis treatment. Enzymatically produced H₂S by the released ALP was then directed to react with Sn(IV) to engender the ZIS NSs/SnS₂ type-I heterojunction on the FTO/ZIS NSs-Sn(IV) electrode, resulting in a change in the photogenerated electron-hole transfer path of the photoelectrode and reduction in current signaling. Exemplified by heart-type fatty acid binding protein (h-FABP) as a target, the constructed PEC sensor showed good stability and selectivity in a biosensing system. Under optimal conditions, the as-prepared sensing platform displayed high sensitivity for h-FABP with a dynamic linear response range of 0.1-1000 pg/mL and a lower detection limit of 55 fg/mL. This research presents the liposome-mediated PEC immunoassay based on in situ type-I heterojunction establishment, providing a new protocol for analyzing various targets of interest.

CRISPR-Cas12a-mediated label-free electrochemical aptamer-based sensor for SARS-CoV-2 antigen detection

Serological antigen testing has emerged as an important diagnostic paradigm in COVID-19, but often suffers from potential cross-reactivity. To address this limitation, we herein report a label-free electrochemical aptamer-based sensor for the detection of SARS-CoV-2 antigen by integrating aptamer-based specific recognition with CRISPR-Cas12a-mediated signal amplification. The sensing principle is based on the competitive binding of antigen and the preassembled Cas12a-crRNA complex to the antigen-specific aptamer, resulting in a change in the collateral cleavage activity of Cas12a. To further generate an electrochemical signal, a DNA architecture was fabricated by in situ rolling circle amplification on a gold electrode, which serves as a novel substrate for Cas12a. Upon Cas12a-based collateral DNA cleavage, the DNA architecture was degraded, leading to a significant decrease in impedance that can be measured spectroscopically. Using SARS-CoV-2 nucleocapsid antigen as the model, the proposed CRISPR-Cas12a-based electrochemical sensor (CRISPR-E) showed excellent analytical performance for the quantitative detection of nucleocapsid antigen. Since in vitro selection can obtain aptamers selective for many SARS-CoV-2 antigens, the proposed strategy can expand this powerful CRISPR-E system significantly for quantitative monitoring of a wide range of COVID-19 biomarkers.

CRISPR/Cas12a collateral cleavage activity for an ultrasensitive assay of RNase H

We herein describe an ultrasensitive RNase H assay by utilizing CRISPR/Cas12a collateral cleavage activity. Based on this unique design principle, the RNase H activity was successfully determined down to 0.00024 U mL^-1, which is quite superior to those of alternative approaches.