DNA tetrahedron-based CRISPR bioassay for treble-self-amplified and multiplex HPV-DNA detection with elemental tagging

CRISPR/Cas Multiplexed Biosensing: Advances, Challenges, and Perspectives

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein systems are renowned for their high sensitivity and specificity, enabling them as a powerful diagnostic toolbox. Multiplexed detection of panels of targets, as opposed to single targets, is imperative for reliable and conclusive disease diagnostics. However, multiplex application of the CRISPR/Cas system has long been hindered by indistinguishable signals from specific targets due to nonspecific chaotic trans-cleavage. To make a breakthrough, substantial efforts have been devoted to CRISPR/Cas-powered multiplexed biosensing strategies, which consequently experienced rapid development over the past five years. This review systematically summarizes recent advances in CRISPR/Cas multiplexed detection encompassing Cas9, Cas12, and Cas13. Key focus issues include multiplex biosensing strategies and their respective advantages and limitations, sensing mechanisms, and detection performance of novel validated examples. Finally, the status and challenges of CRISPR/Cas multiplexed biosensing are critically discussed, and future outlooks are proposed for their potential practical application. This Perspective aims to inspire significant research and promote the development of the next generation of CRISPR/Cas multiplexed biosensing.

CRISPR Digital Sensing: From Micronano-Collaborative Chip to Biomolecular Detection

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) sensing technology proved to be valuable during the COVID-19 pandemic through its sensitivity, specificity, robustness, and versatility. However, issues such as overreliance on amplification, susceptibility to false positives, lack of quantification strategies, and complex operation procedures have hindered its broader application in bioanalysis and clinical diagnostics. The collision between micronano-collaborative chips and CRISPR technology has effectively addressed these bottlenecks, offering innovative solutions for diagnosis and treatment. Unlike conventional micronano chips, micronano digital chips enhance CRISPR's response to trace amounts of target molecules by leveraging highly controllable local environments and compartmentalized microreactors. This advancement improves detection efficiency and revolutionizes traditional in vitro bioanalytical processes. First, the working principles, fabrication techniques, and performance metrics of CRISPR-based digital droplet microfluidics and microarray chips are examined. Then, the applications of CRISPR digital sensing chips in bioassays are reviewed, emphasizing their importance in advancing in vitro detection systems for gene editing. Finally, the prospects of CRISPR digital sensing technology are explored, particularly its potential for body surface biomonitoring and its broader development opportunities in the biomedical field.

Single nanoparticle analysis-based CRISPR/Cas12 bioassay for amplification-free HIV detection

To reduce the "window period" in HIV detection, most analytical methods require additional enzymes for signal amplification. Exempting challenges like primer interference and false positives in amplification strategies, we developed an amplification-free bioassay that uses CRISPR's potent cleavage activity and the competent sensitivity of single-nanoparticle analysis. An attomolar detection limit was achieved with adequate selectivity. Serum and cell tests confirm the bioassay's accurate and sensitive HIV detection.

Single-Tube Multiplex Detection of High-Risk HPV Subtypes Utilizing Lanthanide Nanoprobes

The detection of human papillomavirus (HPV) and its subtypes is of great significance, as the high expression of multiple high-risk subtypes is often associated with various deadly cancers. The golden standard polymerase chain reaction (PCR) has achieved remarkable success in HPV detection, saving many lives over the past few decades. Despite excellent analytical merits, PCR sometimes faces two challenges in the multiplex detection of HPV subtypes: (1) the commercial fluorescent dyes in a single-tube could occasionally be subject to the spectral overlapping interference; (2) the amplification process may introduce contaminations and false positive signals. Herein, the detection of six high-risk HPV subtypes (HPV-16, HPV-18, HPV-31, HPV-39, HPV-56, and HPV-58) in a single-tube was achieved, utilizing self-synthesized lanthanide nanoprobes (NaTbF4, NaHoF4, NaEuF4, NaPrF4, NaYF4, and NaTmF4). These lanthanide nanoprobes feature a low biological background and high sensitivity due to their high intrinsic metal content, enabling the mass spectrometry-based sensitive detection. The detection limits of as low as 0.07 pM were achieved, eliminating the need for the additional nucleic acid amplification. Furthermore, the proposed method exhibited high accuracy and precision in clinical serum samples across all tested HPV subtypes.

Advancements in functional tetrahedral DNA nanostructures for multi-biomarker biosensing: Applications in disease diagnosis, food safety, and environmental monitoring

Deoxyribonucleic acid (DNA) offers the fundamental building blocks for the precisely controlled assemblies due to its inherent self-assembly and programmability. The tetrahedral DNA nanostructure (TDN) stands out as a widely utilized nanostructure, attracting attention for its high biostability, excellent biocompatibility, and versatile modification sites. The capability of DNA tetrahedron to interact with various signal outputs makes it ideal for developing functional DNA nanostructures in biosensing platforms. This review highlights recent advancements in functional tetrahedral DNA nanostructures (FTDN) for various biomarkers monitoring, including nucleic acid, protein, mycotoxin, agent, and metal ion. Additionally, it discusses the potential of FTDN in the fields of disease diagnosis, food safety, and environmental monitoring. The review also introduces the application of FTDN-based biosensors for simultaneous identification of multiple biomarkers. Finally, challenges and prospects are addressed to provide guidance for the continued development of FTDN-based biosensing platforms.

DNA Tetrahedron-enhanced single-particle counting integrated with cascaded CRISPR Program for ultrasensitive dual RNAs logic sensing

CRISPR-Cas-based technology, emerging as a leading platform for molecular assays, has been extensively researched and applied in bioanalysis. However, achieving simultaneous and highly sensitive detection of multiple nucleic acid targets remains a significant challenge for most current CRISPR-Cas systems. Herein, a CRISPR Cas12a based calibratable single particle counting-mediated biosensor was constructed for dual RNAs logic and ultra-sensitive detection in one tube based on DNA Tetrahedron (DTN)-interface supported fluorescent particle probes coupled with a novel synergistic cascaded strategy between CRISPR Cas13a system and strand displacement amplification (SDA). As expected, our platform enables dual RNA molecules intelligent detection using only one crRNA of Cas13a, achieving a sensitivity enhancement of three orders of magnitude assisted with multiple signal amplification and accurate fluorescence particle counting with DTN mediated nano-biointerface enhancement, compared to traditional bulk Cas13a assays. Moreover, the effectiveness and universality of our strategy are experimentally investigated and demonstrated through the detection of mRNAs (cervical cancer swab clinical samples and cultured cancer cells) and bacterial 16s rRNAs. This work not only proposes a highly promising avenue for designing CRISPR-based multiplex detection systems that excel in ultra-sensitivity, specificity, and clinical molecular diagnostics, but also provide new insights into the potential applications of nanotechnology in molecular diagnostics, functional surface engineering, and interface-mediated bioreactions.

Application of CRISPR-Cas System in Human Papillomavirus Detection Using Biosensor Devices and Point-of-Care Technologies

Human papillomavirus (HPV) is the most common virus for genital tract infections. Cervical cancer ranks as the fourth most prevalent cancer globally, with over 99% of cases in women attributed to HPV infection. This infection continues to pose an ongoing threat to public health. Therefore, the development of rapid, high-throughput, and sensitive HPV detection platforms is important, especially in regions with limited access to advanced medical resources. CRISPR-based biosensors, a promising new method for nucleic acid detection, are now rapidly and widely used in basic and applied research and have received much attention in recent years for HPV diagnosis and treatment. In this review, we discuss the mechanisms and functions of the CRISPR-Cas system, focusing on its applications in HPV diagnostics. The review covers CRISPR technologies such as CRISPR-Cas9, CRISPR-Cas12, and CRISPR-Cas13, along with nucleic acid amplification methods, CRISPR-based signal output systems, and point-of-care testing (POCT) strategies. This comprehensive overview highlights the versatility and potential of CRISPR technologies in HPV detection. We also discuss the numerous CRISPR biosensors developed since the introduction of CRISPR to detect HPV. Finally, we discuss some of the challenges faced in HPV detection by the CRISPR-Cas system.

Prevalence and cognitive factors influencing high-risk HPV infection and cervical diseases in women aged 18-45 in Shijiazhuang city

This study aimed to investigate the prevalence of high-risk human papillomavirus (HPV) infection and the awareness levels regarding cervical diseases among women aged 18-45 in Shijiazhuang city. The objectives were to determine the incidence rates of high-risk HPV infections, analyze the patterns of cervical disease occurrence, and identify the factors influencing awareness within this demographic. A total of 544 women aged 18-45 participated in the study, with 102 testing positive for high-risk HPV infection. A structured questionnaire was administered to evaluate awareness of high-risk HPV and cervical diseases. The survey collected data on infection prevalence, subtype distribution, incidence rates, knowledge levels, and factors affecting awareness related to high-risk HPV infections and cervical health. Among the 544 women screened, 102 (18.75%) were diagnosed with high-risk HPV. HPV-16 emerged as the most prevalent subtype, followed by HPV-52 and HPV-58. Of the positive cases, 38 displayed no signs of intraepithelial neoplasia or malignant lesions, while 38 had atypical squamous epithelium, predominantly associated with HPV-52. Low-grade intraepithelial neoplasia was observed in 15 cases, and high-grade neoplasia was found in 11 cases, both primarily linked to HPV-16. Awareness levels varied, with 87 participants demonstrating low knowledge and 15 showing higher awareness. Logistic regression analysis identified education, occupation, residence, and access to scientific knowledge as significant factors influencing awareness and infection risk (P < .05). The prevalence of high-risk HPV infection among women aged 18-45 in Shijiazhuang city is relatively low, with HPV-16 being the predominant subtype. HPV-16 was strongly associated with cervical epithelial neoplasia and cervical cancer. Targeted educational interventions, particularly for populations with lower education levels and those in rural areas, are recommended to enhance awareness and improve the prevention and control of HPV-related infections and cervical diseases.

CRISPR/Cas12a-Powered Electrochemical Platform for Dual-miRNA Detection via an AND Logic Circuit

The CRISPR/Cas technology shows great potential in molecular detection and diagnostics. However, it is still challenging to detect multiple targets simultaneously using the CRISPR-Cas system. Herein, we ingeniously leverage the synergistic effect of two short single-stranded DNA activators to construct a CRISPR/Cas12a-driven electrochemical sensing platform based on an AND logic circuit ("AND" LC-CRISPR) for the simultaneous detection of dual miRNAs. Specifically, the exponential amplification reaction products triggered by the dual-specific miRNAs are designed as binary inputs to bind with Cas12a/crRNA, forming an AND logic circuit and activating the trans-cleavage ability of the CRISPR-Cas12a system. Subsequently, the hairpin probe biogate on the surface of the functionalized electrochemical signal probe (MB@HP-Fe-MOF) is cleaved by activated Cas12a, leading to the release of the encapsulated electroactive signal molecule methylene blue, thereby generating a strong electrochemical signal. As a result, this "AND" LC-CRISPR sensing platform, requiring only a single crRNA assembled with Cas12a, achieves simultaneous detection of miRNA-155 and miRNA-21 at concentrations as low as 3.2 fM. Moreover, the platform allows easy adjustment of the AND logic circuit inputs according to different detection targets, allowing it to be easily expanded for the analysis and diagnosis of other multibiomarkers. This approach demonstrates promising potential for future applications in intelligent diagnostic medicine.

CRISPR/Cas12a-enhanced DNA nanomachine for multiple respiratory pathogens detection

Respiratory infection caused by pathogens is among the most prevalent health issues affecting people worldwide. Accurate and rapid screening of respiratory pathogens is crucial for selecting appropriate treatments to control epidemics. However, it is often challenged by two aspects: first, the low concentration of pathogens in the early stages of infection; second, the difficulty of analyzing multiple pathogens. Herein, we report a mass spectrometry strategy combining the CRISPR/Cas12a system with DNA nanomachines for respiratory pathogens detection. Thanks to the high sensitivity of the CRISPR/Cas12a-enhanced DNA nanomachine and the multiple analysis of elemental mass spectrometry, the proposed method was successfully applied for clinical sample analysis with a low detection limit of 28 amol, 30 amol, and 38 amol for SARS-CoV-2, influenza A virus subtype H1N1, and Mycoplasma pneumoniae, respectively.

Point-of-care testing diagnosis of African swine fever virus by targeting multiple genes with enzymatic recombinase amplification and CRISPR/Cas12a System

African swine fever virus (ASFV) infection is causing devastating outbreaks globally; pig farming has suffered severe economic losses due to the ASFV. Currently, strict biosecurity control measures can mitigate the incidence of ASF. Rapid, cost-effective, and sensitive detection of ASFV can significantly reduce disease transmission and mortality. CRISPR/Cas-associated proteins can detect polymorphisms with high specificity and sensitivity, making them ideal for detecting pathogens. In this study, based on CRISPR/Cas12a integrated with enzymatic recombinase amplification (ERA) technology, a CRISPR/Cas12a detection system capable of identifying ASFV E183L, K205R, and C962R gene sequences has been developed. The ERA-CRISPR/Cas12a detection system detected ASFV precisely without cross-reactivity with other porcine pathogen templates and with a sensitivity detection limit of 10 copies per reaction; it takes 60 minutes to complete the detection process. In combination with this integrated ERA pre-amplification and Cas12a/crRNA cutting assay, it provides a rapid, straightforward, sensitive, and specific method for ASFV detection in the field.

CRISPR for companion diagnostics in low-resource settings

New point-of-care tests (POCTs), which are especially useful in low-resource settings, are needed to expand screening capacity for diseases that cause significant mortality: tuberculosis, multiple cancers, and emerging infectious diseases. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic (CRISPR-Dx) assays have emerged as powerful and versatile alternatives to traditional nucleic acid tests, revealing a strong potential to meet this need for new POCTs. In this review, we discuss CRISPR-Dx assay techniques that have been or could be applied to develop POCTs, including techniques for sample processing, target amplification, multiplex assay design, and signal readout. This review also describes current and potential applications for POCTs in disease diagnosis and includes future opportunities and challenges for such tests. These tests need to advance beyond initial assay development efforts to broadly meet criteria for use in low-resource settings.

Pathogen detection via inductively coupled plasma mass spectrometry analysis with nanoparticles

Infections caused by viruses and bacteria pose a significant threat to global public health, emphasizing the critical importance of timely and precise detection methods. Inductively coupled plasma mass spectrometry (ICP-MS), a contemporary approach for pathogen detection, offers distinct advantages such as high sensitivity, a wide linear range, and multi-index capabilities. This review elucidates the underexplored application of ICP-MS in conjunction with functional nanoparticles (NPs) for the identification of viruses and bacteria. The review commences with an elucidation of the underlying principles, procedures, target pathogens, and NP requirements for this innovative approach. Subsequently, a thorough analysis of the advantages and limitations associated with these techniques is provided. Furthermore, the review delves into a comprehensive examination of the challenges encountered when utilizing NPs and ICP-MS for pathogen detection, culminating in a forward-looking assessment of the potential pathways for advancement in this domain. Thus, this review contributes novel perspectives to the field of pathogen detection in biomedicine by showcasing the promising synergy of ICP-MS and NPs.

Label/immobilization-free Cas12a-based electrochemiluminescence biosensor for sensitive DNA detection

Electrochemiluminescence (ECL) is one of the most sensitive techniques in the field of diagnostics. However, they typically require luminescent labeling and electrode surface biological modification, which is a time-consuming and laborious process involving multiple steps and may also lead to low reaction efficiency. Fabricating label/modification-free biosensors has become one of the most attractive parts for simplifying the ECL assays. In this work, the ECL luminophores carbon dots (CDs) were encapsulated in DNA hydrogel in situ by a simple rolling circle amplification (RCA) reaction. Upon binding of the target DNA, active Cas12a induces a collateral cleavage of the hydrogel's ssDNA backbone, resulting in a programmable degradation of the hydrogel and the release of CDs. By directly measuring the released CDs ECL, a simple and rapid label/modification-free detection of the target HPV-16 was realized. It is noted that this method allowed for 0.63 pM HPV-16 DNA detection without any amplification step, and it could take only ∼60 min for a fast test of a human serum sample. These results showed that our label/modification-free ECL biosensor has great potential for use in simple, rapid, and sensitive point-of-care (POC) detection.

Multiplexed Detection Strategies for Biosensors Based on the CRISPR-Cas System

A growing number of applications require simultaneous detection of multiplexed nucleic acid targets in a single reaction, which enables higher information density in combination with reduced assay time and cost. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-Cas system have broad applications for the detection of nucleic acids due to their strong specificity, high sensitivity, and excellent programmability. However, realizing multiplexed detection is still challenging for the CRISPR-Cas system due to the nonspecific collateral cleavage activity, limited signal reporting strategies, and possible cross-reactions. In this review, we summarize the principles, strategies, and features of multiplexed detection based on the CRISPR-Cas system and further discuss the challenges and perspective.

Label-free detection of biomolecules using inductively coupled plasma mass spectrometry (ICP-MS)

Bioassays using inductively coupled plasma mass spectrometry (ICP-MS) have gained increasing attention because of the high sensitivity of ICP-MS and the various strategies of labeling biomolecules with detectable metal tags. The classic strategy to tag the target biomolecules is through direct antibody-antigen interaction and DNA hybridization, and requires the separation of the bound from the unbound tags. Label-free ICP-MS techniques for biomolecular assays do not require direct labeling: they generate detectable metal ions indirectly from specific biomolecular reactions, such as enzymatic cleavage. Here, we highlight the development of three main strategies of label-free ICP-MS assays for biomolecules: (1) enzymatic cleavage of metal-labeled substrates, (2) release of immobilized metal ions from the DNA backbone, and (3) nucleic acid amplification-assisted aggregation and release of metal tags to achieve amplified detection. We briefly describe the fundamental basis of these label-free ICP-MS assays and discuss the benefits and drawbacks of various designs. Future research is needed to reduce non-specific adsorption and minimize background and interference. Analytical innovations are also required to confront challenges faced by in vivo applications.

An APE1 gated signal amplified biosensor driven by catalytic hairpin assembly for the specific imaging of microRNA in situ

In situ imaging of microRNA (miRNA) content and distribution is valuable for monitoring tumor progression. However, tumor specific in situ imaging remains a challenge due to low miRNA abundance, lack of biological compatibility, and poor specificity. In this study, we designed a DNA tetrahedral framework complex with hairpins (DTF-HPAP) consisting of an apurinic/apyrimidinic site (AP site) that could be specifically recognized and cleaved by apurinic/apyrimidinic endonuclease 1 (APE1). Efficient and specific in situ imaging of miR-21 in tumors was thus achieved through catalytic hairpin assembly (CHA) reaction. In this study, DTF-HPAP was successfully constructed to trigger the cumulative amplification of fluorescence signal in situ. The specificity, sensitivity and serum stability of DTF-HPAP were verified in vitro, and DTF-HPAP could be easily taken up by cells, acting as a biosensor to detect tumors in mice. Furthermore, we verified the ability of DTF-HPAP to specifically image miR-21 in tumors, and demonstrated its capability for tumor-specific imaging in clinical samples.

PER-CRISPR/Cas14a system-based electrochemical biosensor for the detection of ctDNA EGFR L858R

The detection of epidermal growth factor receptor (EGFR) mutation L858R in circulating tumor DNA (ctDNA) is beneficial for the clinical diagnosis and personalized therapy of non-small cell lung cancer (NSCLC). Herein, for the first time, the combination of the primer exchange reaction (PER) and clustered regularly interspaced short palindromic repeats (CRISPR) and its associated nucleases (Cas) 14a was used in electrochemical biosensor construction for the detection of ctDNA EGFR L858R. EGFR L858R, as the target, induced the isothermal amplification of the PER reaction, and then the CRISPR/Cas14a system was activated; subsequently, the substrate ssDNA-MB was cleaved and the electron on the surface of the gold electrode transferred, resulting in the fluctuation of the electrochemical redox signal on the electrode surface, whereas the electrochemical signal will be stable when EGFR L858R is absent. Therefore, the concentration of EGFR L858R can be quantified by electrochemical signal analysis. The low detection limit is 0.34 fM and the dynamic detection range is from 1 fM to 1 μM in this work. The PER-CRISPR/Cas14a electrochemical biosensor greatly improved the analytical sensitivity. In addition, this platform also exhibited excellent specificity, reproducibility, stability and good recovery. This study provides an efficient and novel strategy for the detection of ctDNA EGFR L858R, which has great potential for application in the diagnosis and treatment of NSCLC.