Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application

Dual-palindrome-incorporated hand-in-hand self-linking bidirectional DNA amplifier within exogenous near-infrared light stimulation for high-performance imaging in living biosystems

Although the potency of DNA amplifiers-constructed biosensors for imaging disease biomarkers in living biosystems, they continue to face two challenges: (i) intricate multi-pathway amplification cascades in biosensing designs and (ii) suboptimal detection precision due to uncontrollable pre-activation during bio-delivery. In this contribution, we have brought the following viable resolutions. First, a catalytic hairpin assembly (CHA) routine is incorporated with a dual-palindrome that works like two pairs of hands to self-link CHA-amplified intermediate nucleic acids units, enabling a streamlined two-round signal intensification to enhance sensitivity. Thereafter, one DNA component is conducted with the insertion of a photocleavage-coupler, by which the biosensor can be precisely stimulated via exogenous 808 nm near-infrared (NIR) light-converted upconversion luminescence to recognize the analysis subjects in a controllable action. With the aim of conceptual presentation, this dual-palindrome-incorporated hand-in-hand self-linking bidirectional DNA amplifier stimulated by exogenous NIR light exhibits ultra-sensitive solution detection of various cancers-associated microRNA-155. More deeply, the biosensing toolbox can serve for high-performance imaging of low-abundance biomarkers at the real-word context of living cells and in vivo, boosting the advancement of DNA amplifiers in medical diagnostics.

Paper-based electrochemiluminescence telomerase activity detection using hybridization chain reaction and CRISPR/Cas12a dual signal amplification

Sensitive telomerase activity detection becomes particularly significance since the important value of it in early cancer diagnosis as a potential biomarker. Herein, we developed a paper-based analytical devices (PADs) for telomerase activity detection, using positively charged Au@luminol nanoparticles ((+)Au@luminol NPs) as electrochemiluminescence (ECL) signal probe coupling with hybridization chain reaction (HCR) and CRISPR/Cas12a dual signal amplification. Firstly, the initial strong ECL signal was obtained based on the electrostatic adsorption of (+)Au@luminol NPs onto the surface of HCR double-stranded hybrid aggregates. In the presence of telomerase, the primer was efficiently elongated with telomeric repeats of (TTAGGG)n to release activator DNA and trigger the CRISPR/Cas12a, which can prevent the happen of HCR and the adsorption of (+)Au@luminol NPs through cleaving the capture probe on the electrode surface, such results directly inducing the decrease of the ECL signal that was proportional to telomerase concentration, due to the efficient signal amplification of HCR and CRISPR/Cas12a, a low detection limit of 2.3 cells/mL for telomerase could be detected. Moreover, the sensor realized the effective application for telomerase extracts analysis in human serum samples, making it possess potential application value for telomerase activity assays in cancer diagnostics.

A cell-free biosensor signal amplification circuit with polymerase strand recycling

Cell-free systems are powerful synthetic biology technologies that can recapitulate gene expression and sensing without the complications of living cells. Cell-free systems can perform more advanced functions when genetic circuits are incorporated. Here we expand cell-free biosensing by engineering a highly specific isothermal amplification circuit called polymerase strand recycling (PSR), which leverages T7 RNA polymerase off-target transcription to recycle nucleic acid inputs within DNA strand displacement circuits. We first construct simple PSR circuits to detect different RNA targets with high specificity. We then interface PSR circuits to amplify signals from allosteric transcription factor-based biosensors for small molecule detection. A double equilibrium model of transcription factor-DNA/ligand binding predicts that PSR can improve biosensor sensitivity, which we confirm experimentally by improving the limits of detection by 10-fold to submicromolar levels for two biosensors. We believe this work expands the capabilities of cell-free circuits and demonstrates PSR's potential for diverse applications in biotechnology.

Advancements in fluorescent nanobiosensors for HPV detection: from integrating nanomaterials to DNA nanotechnology

Human papillomavirus (HPV) is a leading cause of cervical cancer and other malignancies, necessitating the development of highly sensitive and specific detection tools. This review explores recent advancements in fluorescent nanobiosensors (FNBS) for HPV detection, focusing on the integration of nanomaterials and DNA nanotechnology, highlighting their contributions to improving sensitivity, specificity, and point-of-care (POC) usability. The review critically evaluates a range of nanomaterial-based FNBS, including those employing quantum and carbon dots, nanoclusters, nanosheets, and nanoparticles, discussing their underlying signal amplification mechanisms, target recognition strategies, and limitations related to toxicity, stability, and reproducibility. Furthermore, it examines the application of diverse DNA nanotechnology, such as DNA origami, DNAzyme, catalytic hairpin assembly (CHA), hybridization chain reaction (HCR), and DNA hydrogel in improving FNBS performance. It also addresses the current challenges in clinical translation, emphasizing the necessity for large-scale production methods and thorough clinical validation to ensure biosafety. It also outlines the potential of innovative technologies, such as CRISPR-Cas-based diagnostics and artificial intelligence, to further revolutionize HPV detection and enable accessible, cost-effective screening, particularly in resource-limited settings. This review provides a valuable resource for researchers and clinicians seeking to develop next-generation FNBS for improved HPV diagnostics and cervical cancer prevention.

CRISPR/Cas-powered nucleic acid amplification and amplification-free biosensors for public safety detection: Principles, advances and prospects

Rapid, accurate, cost-effective, and efficient ultrasensitive detection strategies are essential for public health safety (including food safety, disease prevention and environmental governance). The CRISPR/CRISPR-associated (Cas) detection is a cutting-edge technology that has been widely used in the detection of public health safety due to its targeted cleavage properties (signal amplification), attomolar level sensitivity, high specificity (recognizing single-base mismatches), and rapid turnover time. However, the current research about CRISPR/Cas-based biosensors is not clear, such as mechanism problem and application differences of integrating CRISPR/Cas system with other technologies, and how to further innovate and develop in the future. Therefore, further detailed analysis and comparative discussion of CRISPR/Cas-based biosensors is needed. Currently, CRISPR/Cas system powered biosensors can be mainly categorized into two types: CRISPR/Cas system powered nucleic acid amplification biosensors and CRISPR/Cas system powered nucleic acid amplification-free biosensors. The two biosensors have different characteristics and advantages. This paper first provides an in-depth investigation of the enzymatic mechanism of CRISPR/Cas system at the molecular level. Then, this paper summarizes the principles and recent advances of CRISPR/Cas system powered nucleic acid amplification biosensors and CRISPR/Cas system powered nucleic acid amplification-free biosensors and discusses their integration mechanisms in depth. More, the differences and application-oriented between the two biosensors are further discussed. Finally, the application orientation and future perspectives of the two biosensors are discussed, and unique insights into the future development of CRISPR/Cas system are provided.

A novel self-autocatalytic DNAzyme and catalytic hairpin assembly molecular circuit for highly sensitive and non-label fluorescence aptamer glypican-3 assay

Glypican-3 (GPC-3) is universally regarded as an early diagnostic biomarker and plays a crucial role in the sensitive detection and treatment efficacy evaluation of hepatocellular carcinoma (HCC). Here, a novel self-autocatalytic DNAzyme reaction and catalytic hairpin assembly (CHA)-integrated molecular circuit amplification strategy is developed for realizing an aptamer-based, enzyme- and non-label fluorescence assay of GPC-3. The sensing protocol involves GPC-3 analyte binding to the aptamer in aptamer/ssDNA to trigger the liberation of ssDNA for the initiation of CHA formation of duplexes containing both active DNAzyme and G-quadruplex fragments. The DNAzymes further cleave another G-quadruplex- and DNAzyme-caged signal hairpin to free these sequences to trigger the self-autocatalytic circuit process, which leads to the cyclic cutting of signal hairpins to yield large amounts of G-quadruplexes. Subsequent binding of thioflavin T dye to formed G-quadruplexes thus generates significantly intensified fluorescence signals for detecting GPC-3, with a 0.16 pM detection limit between 1 pM and 100 nM. Moreover, the ability of this method to distinguish GPC-3 from non-target proteins and its success in detecting GPC-3 at low levels in diluted human serum is examined, underscoring its promising potential for monitoring disease-specific biomarkers at trace concentrations for early disease diagnosis.

Tethered Catalytic Hairpin Assembly with Plasmon-Enhanced Fluorescence Readout for Single Molecule Detection

Here a novel digital bioassay readout concept is reported that does not rely on enzymatic amplification nor compartmenting of an analyzed liquid sample. Rather, it is based on counting individual affinity-captured target biomolecules via the use of a tethered catalytic hairpin assembly (tCHA) deployed on a solid sensor surface with spatial confinement utilized by a flexible polymer linker (FPL). Wide-field plasmon-enhanced fluorescence (PEF) imaging is employed for optical real-time probing of the reaction kinetics, where affinity-captured target molecules are manifested as spatially distinct bright fluorescent spots. The effect of the length of the FPLs is investigated, and the analytical performance of the dual amplification tCHA-PEF concept is tested by using a model short single-stranded DNA analyte. When applied in a sandwich immunoassay, the detection of target proteins at sub-femtomolar concentrations is demonstrated. The reported experiments are supported by diffusion-limited mass transfer models and document the potential of tCHA-PEF as a new class of generic enzyme-free bioanalytical tools enabling the ultrasensitive analysis of trace amounts of protein and nucleic acid analytes, making it attractive for future molecular diagnostics and research applications.

Dual-Accelerated Signal Amplification in Biosensing via Spatial Confining Catalytic Hairpin Assembly-Activated Spherical CRISPR/Cas12a System for Trans-Cleavage of Hairpin DNA Reporters

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression and are implicated in various diseases, including cancer. Due to their critical role in diagnostics, there is a growing need for sensitive, specific, and rapid detection methods for miRNAs. In this study, we present a dual-accelerated signal amplification platform for miRNA biosensing, which integrates spatial confining catalytic hairpin assembly (SC-CHA) with spherical CRISPR/Cas12a (S-CRISPR/Cas12a) system for (SC-CHA@S-CRISPR/Cas12a) trans-cleavage of hairpin DNA reporters. The method employs a biotinylated palindrome-rich assembly sequence (PAS) to form DNA nanoballs, which serve as a scaffold for the operation of SC-CHA upon miRNA binding. The SC-CHA products bind with crRNA and Cas 12a protein, activating S-CRISPR/Cas12a system to cleave the hairpin DNA reporter and generate a detectable fluorescence signal. The uniqueness of this system lies in the combined use of DNA nanoballs and hairpin DNA reporters, both of which significantly accelerate reaction kinetics, resulting in rapid signal generation. Additionally, the spherical DNA nanostructure, integrated with the S-CRISPR/Cas12a system, greatly enhances biostability and accelerating reaction kinetics. These features enable the platform to exhibit high sensitivity, with a limit of detection (LOD) as low as 13.75 fM, and excellent specificity, successfully distinguishing miRNA-21 from other miRNAs. The assay is also biostable, demonstrating reliable performance in complex biological samples such as human serum. This dual-acceleration approach offers a promising solution for sensitive, rapid, and specific miRNA biosensing, with potential applications in early cancer diagnosis and clinical monitoring.

Exploring the frontiers of emerging sensing of silver nanoprisms: recent progress and challenges

In recent years, the development and use of nanomaterials have transformed numerous aspects of biomedical science. Nanomaterials have played a pivotal role in advancing disease diagnosis and treatment across a wide range of applications. Within this scope, silver nanoprisms (AgNPrs) stand out due to their remarkable properties, such as extensive surface area, chemical robustness, and tunable electrical conductivity, making them excellent candidates for biomedical purposes. By tailoring these nanomaterials through functionalization or coating surface, their multifunctionality can be enhanced, unlocking new opportunities for their application in areas such as diagnosis, imaging, and therapeutic intervention. This review begins with an overview of AgNPrs' synthesis techniques and their unique physicochemical characteristics. Recent advancements in analytical methods utilizing AgNPrs, categorized by sensing mechanisms such as optical and electrochemical approaches, are highlighted in the context of diagnostics. Lastly, the challenges and future prospects of bringing AgNPr-based technologies to commercialization and integrating them into disease diagnostics and medical treatment are explored. The integration of AgNPrs in disease therapy holds promise for the development of advanced chemotherapy agents that effectively address the challenges of efficient cancer treatment looking ahead, the ongoing advancement of nanocarrier systems comprising AgNPrs-based molecules holds great promise for improving the quality of life for patients worldwide.

Dual-Functional Aptasensor for the Detection and Inactivation of Salmonella Based on Cascade Signal Amplification Coupled with Ag-Pt Nanozymes

The establishment of a pathogen monitoring platform that integrates detection and disinfection can effectively reduce the risk of secondary pollution. Herein, we report a dual-functional aptasensor for ultrasensitive detection and efficient inactivation of Salmonella based on cascade signal amplification and nucleic-acid-templated silver-platinum (Ag-Pt) nanozymes. Specifically, in the presence of Salmonella, the method promotes an exponential amplification reaction (EXPAR) and automatic assembly circuit (AAC) reaction by aptamer targeting bacteria, accompanied by an exponentially magnified "turn-on" fluorescence. Concurrently, guided by an aptamer, Ag-Pt nanozymes attached to the surface of Salmonella can catalyze H2O2 to produce reactive oxygen species and effectively inactivate Salmonella. The aptasensor shows good specificity and sensitivity, with a linear range of 2 × 100-2 × 105 CFU/mL and a detection limit of 2 × 100 CFU/mL. Besides, it was applied in the detection of milk, and satisfactory results were obtained. The strategy offers a robust solution for early pathogen detection and control in food safety.

Gold Nanorod Nanolayer-Mediated Photothermal Transfection Promotes DNA Nanomachine Crossing of Cell Membranes for Sensitive Cell Imaging

The transmembrane efficiency of DNA nanomachines greatly affects the performance of cell imaging. The current transmembrane methods suffer from long time incubation, low efficiency, and potential cyto-toxicity. Here, we report on a novel gold nanorod nanolayer-mediated photothermal transfection (AuNRs-NMPT) method to deliver a DNA nanomachine across the cell membrane. Due to good photothermal effects, AuNRs nanolayer-functionalized slide (AuNRs-NFS) converted light energy into local heat. Local heat disrupted the fluidity of the cell membrane for perforation. The DNA nanomachine penetrates the cell membrane rapidly and efficiently via those holes under the optimal laser power and irradiation time. The AuNRs-NMPT exhibited a 12-fold lower incubation time and 13-fold higher fluorescent intensity compared to that of common direct incubation. The cells also exhibited a high cell viability after being treated with the AuNRs-NMPT, due to cell membrane self-repair. Due to efficient, rapid, and low cytotoxic transmembrane transfection, the AuNRs-NMPT ensures sensitive cell imaging of miRNA-21. The proposed AuNRs-NMPT will promote the application of DNA nanomachines for clinical cancer diagnosis in the future.

A Dual-Cycle Isothermal Amplification Method for microRNA Detection: Combination of a Duplex-Specific Nuclease Enzyme-Driven DNA Walker with Improved Catalytic Hairpin Assembly

The association between microRNAs and various diseases, especially cancer, has been established in recent years, indicating that miRNAs can potentially serve as biomarkers for these diseases. Determining miRNA concentrations in biological samples is crucial for disease diagnosis. Nevertheless, the stem-loop reverse transcription quantitative PCR method, the gold standard for detecting miRNA, has great challenges in terms of high costs and enzyme limitations when applied to clinical biological samples. In this study, an isothermal signal amplification method based on a duplex-specific nuclease (DSN) enzyme-driven DNA walker and an improved catalytic hairpin assembly (CHA) was designed for miRNA detection. First, biotin-triethylene glycol-modified trigger-releasable DNA probes were conjugated to the streptavidin-coated magnetic beads for recognizing the target miRNA. The DSN enzyme specifically hydrolyzes DNA strands when the DNA probe hybridizes with the targeted miRNA. This recycling process converts the input miRNA into short trigger fragments (catalysts). Finally, three hairpins of improved CHA are driven by this catalyst, resulting in the three-armed CHA products and a fluorescence signal as the output. This dual-cycle biosensor shows a good linear relationship in the detection of miR-21 and miR-141 over the final concentration range of 250 fM to 50 nM, presenting an excellent limit of detection (2.95 amol). This system was used to detect miR-21 and miR-141 in MCF-7 and 22RV1 cells, as well as in 1% human serum. This system can be used to evaluate the expression levels of miRNAs in different biological matrices for the clinical diagnosis and prognosis of different cancers.

Highly sensitive fluorescence detection of chloramphenicol based on product catalysis of tetrahedral DNA framework and fluorescent quenching of MIL-101(Fe)

An ultrasensitive fluorescence detection strategy of chloramphenicol (CAP) was developed based on product catalysis of tetrahedral DNA framework (TDF) and fluorescent quenching of MIL-101(Fe). The product was used to catalyze the reaction. As the concentration of catalyst increased, the reaction time was significantly shorted to 21 min which was much shorter than other isothermal amplification technologies. Moreover, the multiple fluorophores of TDF and high efficient quenching ability of MIL-101(Fe) provided better performance with a linear range for CAP detecting from 1.6 pM to 80 pM and the limit of detection (LOD) as low as 0.67 pM. In addition, it also demonstrated good specificity and resistance to interference from other related antibiotics. Importantly, this strategy exhibited satisfactory relative standard deviation and recovery results for practical application, exhibiting a favorable application prospect in CAP analysis.

Proximity hybridization-triggered cascade amplification for label-free SERS detection of Alzheimer's amyloid-β oligomers

Most of the existing SERS systems failed to achieve satisfactory results in early diagnosis of Alzheimer's disease owing to a lack of effective signal transduction. Herein, we developed a dual signal amplification strategy for SERS detection of amyloid-β oligomers based on proximity hybridization-triggered catalyzed hairpin assembly (CHA) and hybridization chain reaction (HCR). In the presence of the target protein and two DNA-labeled antibodies, a proximate complex formed in a homogeneous solution. Each of the AβO-DNA complexes served as a catalyst to trigger and accelerate numerous hybridization processes between MB1 and MB2. Subsequently, the single-strand fragment on the electrode surface initiated HCR, resulting in the hybridization reaction to form double-strand DNA concatemers on the substrate surface. The surface became negatively charged and allowed the absorption of silver ions on the DNA skeleton. After chemical reduction by hydroquinone, the formed silver nanoparticles could be further grown with a silver enhancement step to amplify the detectable SERS signal by absorbing rhodamine 6G as a SERS reporter on the silver nanoparticle surface. This biosensing platform had potential applications in molecular diagnostics of AD serum samples.

A dual-mode strategy for early detection of sugarcane pokkah boeng disease pathogen: A portable sensing device based on Cross-N DNA framework and MoS2@GDY

Sucrose, a common sugar primarily derived from sugarcane, is a crucial national strategic resource. However, its yield is significantly affected by various serious diseases, with pokkah boeng disease being one of the most damaging. Therefore, developing a sensitive method for the accurate detection of the pokkah boeng disease pathogen is crucial for ensuring the safety of sugar. This work presents a portable dual-modal detection device, assisted by a smartphone, which is based on MoS2@GDY, Mn3O4@Au nanomenzyme, cross-N DNA framework and Exo III exonuclease-assisted CHA signal amplification technology. The cross-N DNA framework provides many binding sites and is not restricted by AuNPs scattering positions, enhancing the signal output strength of the sensor. Additionally, the detection system incorporates a high-power-density capacitor to further amplify the electrochemical detection signal, increasing sensitivity by 9.1 times. Moreover, the use of electrochemical and colorimetric dual-mode detection effectively avoids mutual interference, reducing the likelihood of false positives from a single signal. Under optimized conditions, the proposed method has a linear range of 0.0001-10,000 pM, and with a detection limit of 6.1 aM (S/N=3). This high-sensitivity, high-reliability portable sensing method shows significant potential for the early detection and real-time on-site monitoring of the pokkah boeng disease pathogen.

Reversible addition-fragmentation chain transfer enhanced aggregation signal-on fluorescence detection of alkaline phosphatase

The instability of the signal intensity of fluorescent biosensors and the false signals have been significant factors affecting the performance of biosensors. Herein, a novel signaling system is devised through the application of reversible addition-fragmentation chain transfer (RAFT) polymerization with monomers containing the tetraphenylethylene (TPE) groups. TPE exhibits an aggregation-induced emission (AIE) phenomenon in certain solvents, mainly due to the blockage of the rotation of its four benzene rings, which also exist in the aggregated state. With this property, a series of molecules are modified based on click chemistry for RAFT polymerization using Fe3O4 magnetic beads as the carriers, and stable aggregated luminescent TPE polymers are formed on the surface of magnetic beads to realize the transformation of fluorescence signal from "0" to "1". In addition, the fluorescence signal demonstrates a positive correlation with alkaline phosphatase (ALP) activity, which can be quantified by measuring the fluorescence intensity. The biosensor exhibits high sensitivity and good linearity in the range of 0.1-5 U/L, with a LOD of 0.079 U/L. Furthermore, the designed strategy demonstrated satisfactory performance in the quantitative determination of ALP activity in serum samples, indicating that the signaling system developed by combining RAFT polymerization and AIE molecules has an important application in the field of fluorescent biosensors.

Advances in novel biosensors in biomedical applications

Biosensors, devices capable of detecting biomolecules or bioactive substances, have recently become one of the important tools in the fields of bioanalysis and medical diagnostics. A biosensor is an analytical system composed of biosensitive elements and signal-processing elements used to detect various biological and chemical substances. Biomimetic elements are key to biosensor technology and are the components in a sensor that are responsible for identifying the target analyte. The construction methods and working principles of biosensors based on synthetic biomimetic elements, such as DNAzyme, molecular imprinted polymers and aptamers, and their updated applications in biomedical analysis are summarised. Finally, the technical bottlenecks and future development prospects for biomedical analysis are summarised and discussed.

DNA Nanomaterial-Based Electrochemical Biosensors for Clinical Diagnosis

Sensitive and quantitative detection of chemical and biological molecules for screening, diagnosis and monitoring diseases is essential to treatment planning and response monitoring. Electrochemical biosensors are fast, sensitive, and easy to miniaturize, which has led to rapid development in clinical diagnosis. Benefiting from their excellent molecular recognition ability and high programmability, DNA nanomaterials could overcome the Debye length of electrochemical biosensors by simple molecular design and are well suited as recognition elements for electrochemical biosensors. Therefore, to enhance the sensitivity and specificity of electrochemical biosensors, significant progress has been made in recent years by optimizing the DNA nanomaterials design. Here, the establishment of electrochemical sensing strategies based on DNA nanomaterials is reviewed in detail. First, the structural design of DNA nanomaterial is examined to enhance the sensitivity of electrochemical biosensors by improving recognition and overcoming Debye length. In addition, the strategies of electrical signal transduction and signal amplification based on DNA nanomaterials are reviewed, and the applications of DNA nanomaterial-based electrochemical biosensors and integrated devices in clinical diagnosis are further summarized. Finally, the main opportunities and challenges of DNA nanomaterial-based electrochemical biosensors in detecting disease biomarkers are presented in an aim to guide the design of DNA nanomaterial-based electrochemical devices with high sensitivity and specificity.

Hairpin self-assembly powered by exonuclease III for highly sensitive and cross-validated miRNA-155 detection

Cancer is one of the most important causes of human death and poses a serious threat to human health. As a cancer biomarker, microRNA-155 (miRNA-155) is highly expressed in various types of cancer tissues and is involved in the proliferation of tumor cells. Therefore, developing a miRNA-155 detection technology with high specificity and sensitivity is of great significance for the early detection, accurate treatment and prognostic evaluation of tumors. Here, we developed a fluorescence detection method using exonuclease III-assisted target cycling and catalytic hairpin assembly (CHA) as a signal amplification technique. This study developed a biosensor for the detection of miRNA-155, utilizing a DNA hairpin (Hp) for target recognition and generating double-stranded DNA (dual-Hp-T). The 3' flat end of the double-stranded DNA can be cleaved by exonuclease III to achieve the target cycle, and a large amount of single-stranded DNA (fuel) can trigger CHA to achieve signal amplification. Simultaneously, the fluorescence resonance energy transfer (FRET) of signal probes with different fluorescence labels on H1 and H2 ends occurs with the CHA reaction. The two fluorescence signals obtained can be used to cross-validate the experimental results. The biosensor exhibits excellent performance of high recovery, high sensitivity and high operability, which can achieve the specific detection of miRNA-155 with a detection limit as low as 8.3 pM. Additionally, the detection efficacy in a human serum environment is also highly satisfactory. This technology provides strong technical support for the development of nucleic acid probes and the diagnosis and treatment of cancer, demonstrating significant practical application value.

Nucleic acid-functionalized gold nanoparticles as intelligent photothermal therapy agents for precise cancer treatment

We present an intelligent photothermal therapy agents by functionalizing gold nanoparticles with specific nucleic acid sequences. Hairpin nucleic acids are modified to the nanoparticles, forming AuNPs-1 and AuNPs-2. Upon infiltrating cancer cells, these nanoparticles undergo catalytic hairpin assembly in the presence of target miRNA, leading to aggregation and subsequent photothermal conversion. Under near-infrared laser irradiation, aggregated gold nanoparticles exhibit efficient photothermal conversion, selectively damaging cancer cells. This approach offers heightened selectivity, as nanoparticles only aggregate in environments with cancer biomarkers present, sparing normal cells. Cytotoxicity assays confirm minimal toxicity to normal cells. In vivo studies on mice bearing solid tumors validate the system's efficacy in tumor regression. Overall, this study highlights the potential of nucleic acid-functionalized gold nanoparticles in intelligent and selective cancer photothermal therapy, offering insights for targeted diagnosis and treatment development.

A non-enzymatic, isothermal amplification sensor for quantifying the relative abundance of Akkermansia muciniphila

Herein, we have developed a non-enzymatic, isothermal amplification assay (NIA sensor) based on a catalytic hairpin assembly (CHA) reaction for quantifying the relative abundance of Akkermansia muciniphila. Through detection of the MUC-1437 gene (limit of detection: 8.3 fM) in a dynamic range from 10 fM to 1 nM, the NIA sensor shows high sensitivity and selectivity in preclinical models of mice fed a normal or high-fat diet (HFD), and treated with antibiotics (ATB). The NIA sensor, which operates without the use of any enzymes, leading to simplicity and cost-effectiveness, has great potential for biosensing research and clinical diagnostic applications.

Hybrid chain reaction nanoscaffold-based functional nucleic acid nanomaterial cascaded with rolling circle amplification for signal enhanced miRNA let-7a detection

A novel functional nucleic acid (FNA) nanomaterial based on hybrid chain reaction (HCR) nanoscaffolds is proposed to solve the problem of time superposition and repeated primer design in sensitive miRND detection using cascade amplification technique. Rolling circle amplification (RCA) was cascaded with the prepared FNA nanomaterials for miRNA let-7a (as a model target) sensitive detection by lateral flow assay (LFA). Under the optimal conditions, the proposed RCA-FNA-LFA assay demonstrated the specificity and accuracy for miRNA let-7a detection with a detection limit of 1.07 pM, which increased sensitivity by nearly 20 times compared with that of RCA -LFA assay. It is worth noting that the non-target-dependent self-assembly process of HCR nanoscaffolds does not take up the whole detection time, thus, less time is taken than that of the conventional cascaded method. Moreover, the proposed assay does not need to consider the system compatibility between two kinds of isothermal amplification techniques. As for detection of different miRNAs, only the homologous arm of the padlock probe of RCA needs to be changed, while the FNA nanomaterial does not need any change, which greatly simplifies the primer design of the cascaded amplification techniques. With further development, the proposed RCA-FNA-LFA assay might achieve more sensitive and faster results to better satisfy the requirements of clinical diagnosis combing with more sensitive labels or small strip reader.

Enzyme-free and rapid colorimetric analysis of osteopontin via triple-helix aptamer probe coupled with catalytic hairpin assembly reaction

BACKGROUND

Osteopontin (OPN) is closely associated with tumorigenesis, growth, invasion, and immune escape and it serves as a plasma biomarker for hepatocellular carcinoma (HCC). Nevertheless, the accurate and rapid detection of low-abundance OPN still poses significant challenges. Currently, the majority of protein detection methods rely heavily on large precision instruments or involve complex procedures. Therefore, developing a simple, enzyme-free, rapid colorimetric analysis method with high sensitivity is imperative.

RESULTS

In this study, we have developed a portable colorimetric biosensor by integrating the triple-helix aptamer probe (THAP) and catalytic hairpin assembly (CHA) strategy, named as T-CHA. After binding to the OPN, the trigger probe can be released from THAP, then initiates the CHA reaction and outputs the signal through the formation of a G-quadruplex/Hemin DNAzyme with horseradish peroxidase-like activity. Consequently, this colorimetric sensor achieves visual free-labeled detection without additional fluorophore modification and allows for accurate quantification by measuring the optical density of the solution at 650 nm. Under optimal conditions, the logarithmic values of various OPN concentrations exhibit satisfactory linearity in the range of 5 pg mL-1 to 5 ng mL-1, with a detection limit of 2.04 pg mL-1. Compared with the widely used ELISA strategy, the proposed T-CHA strategy is rapid (∼105 min), highly sensitive, and cost-effective.

SIGNIFICANCE

The T-CHA strategy, leveraging the low background leakage of THAP and the high catalytic efficiency of CHA, has been successfully applied to the detection of OPN in plasma, demonstrating significant promise for the early diagnosis of HCC in point-of-care testing. Given the programmability of DNA and the universality of T-CHA, it can be readily modified for analyzing other useful tumor biomarkers.

Leveraging Concentration Imbalance-Driven DNA Circuit as an Operational Amplifier to Enhance the Sensitivity of Hepatitis B Virus DNA Detection with Hybridization-Responsive DNA-Templated Silver Nanoclusters

Hepatitis B virus (HBV) infection remains a major global health concern, necessitating the development of sensitive and reliable diagnostic methods. In this study, we propose a novel approach to enhance the sensitivity of HBV DNA detection by leveraging a concentration imbalance-driven DNA circuit (CIDDC) as an operational amplifier, coupled with a hybridization-responsive DNA-templated silver nanocluster (DNA-AgNCs) nanoprobe named Q·C6-AgNCs. The CIDDC system effectively converts and amplifies the input HBV DNA into an enriched generic single-stranded DNA output, which subsequently triggers the fluorescence of the DNA-AgNCs reporter upon hybridization, generating a measurable signal for detection. By incorporating the DNA circuit, we not only achieved enhanced sensitivity with a lower detection limit of 0.11 nM but also demonstrated high specificity with single-base mismatch discriminability for HBV DNA detection. Additionally, this mix-and-detect assay format is simple, user-friendly, and isothermal. This innovative strategy holds promise for advancing molecular diagnostics and facilitating the effective management of HBV-related diseases.

Advancements in Biosensors for Point-of-Care Testing of Nucleic Acid

Rapid, low-cost and high-specific diagnosis based on nucleic acid detection is pivotal in both detecting and controlling various infectious diseases, effectively curbing their spread. Moreover, the analysis of circulating DNA in whole blood has emerged as a promising noninvasive strategy for cancer diagnosis and monitoring. Although traditional nucleic acid detection methods are reliable, their time-consuming and intricate processes restrict their application in rapid field assays. Consequently, an urgent emphasis on point-of-care testing (POCT) of nucleic acids has arisen. POCT enables timely and efficient detection of specific sequences, acting as a deterrent against infection sources and potential tumor threats. To address this imperative need, it is essential to consolidate key aspects and chart future directions in POCT biosensors development. This review aims to provide an exhaustive and meticulous analysis of recent advancements in POCT devices for nucleic acid diagnosis. It will comprehensively compare these devices across crucial dimensions, encompassing their integrated structures, the synthesized nanomaterials harnessed, and the sophisticated detection principles employed. By conducting a rigorous evaluation of the current research landscape, this review will not only spotlight achievements but also identify limitations, offering valuable insights into the future trajectory of nucleic acid POCT biosensors. Through this comprehensive analysis, the review aspires to serve as an indispensable guide for fostering the development of more potent biosensors, consequently fostering precise and efficient POCT applications for nucleic acids.

Self-assembly of hyperbranched DNA network structure for signal amplification detection of miRNA

Catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR) can achieve the high sensitivity and rapid reaction rate in detecting miRNA. However, the amplification efficiency by these methods are limited. Herein, an enzyme-free and label-free hyperbranched DNA network structure (HDNS) was designed, in which localized catalytic hairpin assembly (LCHA) and hybridization chain reaction occurred in the horizontal axis and longitudinal axis, respectively, exhibiting intensive signal dual-amplification. miRNA-122 was selected as the target on behalf of miRNA to design the HDNS sensor. The fluorescence signal change of HDNS showed good linearity for detecting miRNA-122 in the concentration range from 0.1 nM to 60 nM with a limit of detection (LOD) at 37 pM which was lower than those of the sensors based on separate CHA or HCR. Afterwards, the HDNS sensor was applied to detect miRNA-122 in serum samples with the recovery rate in the range of 97.2 %-107 %. The sensor could distinguish different kinds of miRNAs, even the family members with high sequence homology, exhibiting excellent selectivity. This method provided a novel design strategy for improving the sensitivity and selectivity of DNA sensor for miRNA detection.

Rapid and accurate SERS assay of disease-related nucleic acids based on isothermal cascade signal amplifications of CRISPR/Cas13a system and catalytic hairpin assembly

Developing rapid, accurate and convenient nucleic acid diagnostic techniques is essential for the prevention and control of contagious diseases that are prone to gene mutations and may have homologous sequences, especially emerging infectious diseases such as the SARS-CoV-2 pandemic. Herein, a one-pot SERS assay integrating isothermal cascade signal amplification strategy (i.e., CRISPR/Cas13a system (Cas13a) and catalytic hairpin assembly (CHA), Cas13a-CHA) and SERS-active silver nanorods (AgNRs) sensing chips was proposed for rapid and accurate detection of disease-related nucleic acids. Taking SARS-CoV-2 RNA assay as a model, the Cas13a-CHA based SERS sensing strategy can achieve ultra-high sensitivity low to 5.18 × 102 copies·mL-1 within 60 min, and excellent specificity, i.e., not only the ability to identify SARS-CoV-2 RNA from gene mutations, but also incompatibility with coronaviruses such as severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV), and other respiratory viruses. The proposed Cas13a-CHA based SERS assay for SARS-CoV-2 RNA has satisfactory sensitivity, specificity, uniformity, and repeatability, and can be easily expanded and universalized for screening different viruses, which is expected to promise as a crucial role for diagnosis of disease-related nucleic acids in various medical application scenarios.

Enhanced Aggregation-Induced Delayed Electrochemiluminescence Triggered by Spatial Perturbation of Organic Dots

Development of highly efficient, heavy-metal-free electrochemiluminescence (ECL) materials is attractive but still challenging. Herein, we report an aggregation-induced delayed ECL (AIDECL) active organic dot (OD) composed of a tert-butoxy-group-substituted benzophenone-dimethylacridine compound, which shows high ECL efficiency. The resultant ODs exhibit 2.1-fold higher ECL efficiency compared to control AIDECL-active ODs. Molecular stacking combined with theoretical calculations suggests that tert-butoxy groups effectively participate in the intermolecular interactions, further inhibiting the molecular motions in the aggregated states and thus accelerating radiative decay. On the basis of these ODs exhibiting excellent ECL performance, a proof-of-concept biosensor is constructed for the detection of miR-16 associated with Alzheimer's disease, which demonstrates excellent detection ability with the limit of detection of 1.7 fM. This work provides a new approach to improve the ECL efficiency and enriches the fundamental understanding of the structure-property relationship.

Interface-constrained catalytic hairpin assembly permits highly sensitive SERS signaling of miRNA

The rapid and precise monitoring of peripheral blood miRNA levels holds paramount importance for disease diagnosis and treatment monitoring. In this study, we propose an innovative research strategy that combines the catalytic hairpin assembly reaction with SERS signal congregation and enhancement. This combination can significantly enhance the stability of SERS detection, enabling stable and efficient detection of miRNA. Specifically, our paper-based SERS detection platform incorporates a streptavidin-modified substrate, biotin-labeled catalytic hairpin assembly reaction probes, 4-ATP, and primer-co-modified gold nanoparticles. In the presence of miRNA, the 4-ATP and primer-co-modified gold nanoparticles can specifically recognize the miRNA and interact with the biotin-labeled CHA probes to initiate an interfacial catalytic hairpin assembly reaction. This enzyme-free high-efficiency catalytic process can accumulate a large amount of biotin on the gold nanoparticles, which then bind to the streptavidin on the substrate with the assistance of the driving liquid, forming red gold nanoparticle stripes. These provide a multitude of hotspots for SERS, enabling enhanced signal detection. This innovative design achieves a low detection limit of 3.47 fM while maintaining excellent stability and repeatability. This conceptually innovative detection platform offers new technological possibilities and solutions for clinical miRNA detection.

DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications

The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.

Visually evaluating drug efficacy in living cells using COF-based fluorescent nanoprobe via CHA amplified detection of miRNA and simultaneous apoptosis imaging

BACKGROUNDS

Cancer is a highly fatal disease which is close relative of miRNA aberrant expression and apoptosis disorders. Elucidation of the therapeutic efficacy through investigating the changes in miRNA and apoptosis holds immense importance in advancing the development of miRNA-based precision therapy. However, it remains a challenge as how to visually evaluate the efficacy during protocol optimization of miRNA-based anticancer drugs at the cellular level. Therefore, exploring effective and noninvasive methods for real-time monitoring of therapeutic efficacy in living cells is of great significance.

RESULTS

Herein, we reported a novel fluorescent nanoprobe COF-H1/H2-Peptide for visually evaluating drug efficacy in living cells through amplified imaging of low-abundant miRNA-221 with catalytic hairpin assembly (CHA) circle amplification, as well as simultaneous caspase-3 imaging. With strong stability and good biocompatibility, this newly fabricated amplified nanoprobe showed high sensitivity and specificity for the detection of miRNA-221 and caspase-3, and the limit of detection (LOD) of miRNA-221 was as low as 2.79 pM. The fluorescent imaging results showed that this amplified nanoprobe could not only detect caspase-3 in living cells, but also effectively detect low levels of miRNA-221 with increasing anticancer drug concentration and treatment time. The smart nanoprobe had effective performance for optimizing miRNA-based drug treatment schedules by dual-color fluorescence imaging.

SIGNIFICANCE

This nanoprobe combined CHA amplified detection of intracellular miRNA-221 and synchronous apoptosis imaging, with excellent sensitivity for the detection of cellular low-level miRNA, enabling the realization of real-time assessment of the efficacy of miRNA-based therapy in living cells. This work presents a promising approach for revealing the regulatory mechanisms between miRNAs and apoptosis in cancer occurrence, development, and treatment.

Near-Infrared Light-Powered and DNA Nanocage-Confined Catalytic Hairpin Assembly Nanobiosensor with a Nucleic Acid Restriction Behavior and Reinforced Enzymatic Resistance for Robust Imaging Assay in Live Biosystems

While DNA amplifier-built nanobiosensors featuring a DNA polymerase-free catalytic hairpin assembly (CHA) reaction have shown promise in fluorescence imaging assays within live biosystems, challenges persist due to unsatisfactory precision stemming from premature activation, insufficient sensitivity arising from low reaction kinetics, and poor biostability caused by endonuclease degradation. In this research, we aim to tackle these issues. One aspect involves inserting an analyte-binding unit with a photoinduced cleavage bond to enable a light-powered notion. By utilizing 808 nm near-infrared (NIR) light-excited upconversion luminescence as the ultraviolet source, we achieve entirely a controllable sensing event during the biodelivery phase. Another aspect refers to confining the CHA reaction within the finite space of a DNA self-assembled nanocage. Besides the accelerated kinetics (up to 10-fold enhancement) resulting from the nucleic acid restriction behavior, the DNA nanocage further provides a 3D rigid skeleton to reinforce enzymatic resistance. After selecting a short noncoding microRNA (miRNA-21) as the modeled low-abundance sensing analyte, we have verified that the innovative NIR light-powered and DNA nanocage-confined CHA nanobiosensor possesses remarkably high sensitivity and specificity. More importantly, our sensing system demonstrates a robust imaging capability for this cancer-related universal biomarker in live cells and tumor-bearing mouse bodies, showcasing its potential applications in disease analysis.

Sample-to-answer salivary miRNA testing: New frontiers in point-of-care diagnostic technologies

MicroRNA (miRNA), crucial non-coding RNAs, have emerged as key biomarkers in molecular diagnostics, prognosis, and personalized medicine due to their significant role in gene expression regulation. Salivary miRNA, in particular, stands out for its non-invasive collection method and ease of accessibility, offering promising avenues for the development of point-of-care diagnostics for a spectrum of diseases, including cancer, neurodegenerative disorders, and infectious diseases. Such development promises rapid and precise diagnosis, enabling timely treatment. Despite significant advancements in salivary miRNA-based testing, challenges persist in the quantification, multiplexing, sensitivity, and specificity, particularly for miRNA at low concentrations in complex biological mixtures. This work delves into these challenges, focusing on the development and application of salivary miRNA tests for point-of-care use. We explore the biogenesis of salivary miRNA and analyze their quantitative expression and their disease relevance in cancer, infection, and neurodegenerative disorders. We also examined recent progress in miRNA extraction, amplification, and multiplexed detection methods. This study offers a comprehensive view of the development of salivary miRNA-based point-of-care testing (POCT). Its successful advancement could revolutionize the early detection, monitoring, and management of various conditions, enhancing healthcare outcomes. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.

DNA-Based Nanomaterials for Analysis of Extracellular Vesicles

Extracellular vesicles (EVs) are cell-derived nanovesicles comprising a myriad of molecular cargo such as proteins and nucleic acids, playing essential roles in intercellular communication and physiological and pathological processes. EVs have received substantial attention as noninvasive biomarkers for disease diagnosis and prognosis. Owing to their ability to recognize protein and nucleic acid targets, DNA-based nanomaterials with excellent programmability and modifiability provide a promising tool for the sensitive and accurate detection of molecular cargo carried by EVs. In this perspective, recent advancements in EV analysis using a variety of DNA-based nanomaterials are summarized, which can be broadly classified into three categories: linear DNA probes, DNA nanostructures, and hybrid DNA nanomaterials. The design, construction, advantages, and disadvantages of different types of DNA nanomaterials, as well as their performance for detecting EVs are reviewed. The challenges and opportunities in the field of EV analysis by DNA nanomaterials are also discussed.

Genetically engineered virus-like particle-armoured and multibranched DNA scaffold-corbelled ultra-sensitive hierarchical hybridization chain reaction for targeting-enhanced imaging in living biosystems under spatiotemporal light powering

Although nucleic acids-based fluorescent biosensors, exemplified by the hybridization chain reaction (HCR), have exhibited promise as an imaging tool for detecting disease-related biomolecular makers in living biosystems, they still face certain challenges. These include the need for improved sensitivity, poor bio-targeting capability, the absence of signal enrichment interface and the uncontrollable biosensing initiation. Herein, we present a range of effective solutions. First, a stacking design resembling building blocks is used to construct a special hierarchical HCR (termed H-HCR), for which a hierarchical bridge is employed to graft multiunit HCR products. Furthermore, the H-HCR components are encapsulated into a virus-like particle (VLP) endowed with a naturally peptide-mediated targeting unit through genetic engineering of plasmids, after which the biosensor can specifically identify cancer cytomembranes. By further creating a multibranched DNA scaffold to enrich the H-HCR produced detection signals, the biosensor's analyte recognition module is inserted with a photocleavage-linker, allowing that the biosensing process can be spatiotemporally initiated via a light-powered behavior. Following these innovations, this genetically engineered VLP-armoured and multibranched DNA-scaffold-corbelled H-HCR demonstrates an ultra-sensitive and specific biosensing performance to a cancer-associated microRNA marker (miRNA-155). Beyond the worthy in vitro analysis, our method is also effective in performing imaging assays for such low-abundance analyte in living cells and even bodies, thus providing a roust platform for disease diagnosis.

A highly sensitive colorimetric DNA sensor for MicroRNA-155 detection: leveraging the peroxidase-like activity of copper nanoparticles in a double amplification strategy

A novel and highly sensitive colorimetric DNA sensor for determination of miRNA-155 at attomolar levelsis presented that combines the peroxidase-like activity of copper nanoparticles (CuNPs) with the hybridization chain reaction (HCR) . The utilization of CuNPs offers advantages such as strong interaction with double-stranded DNA, excellent molecular recognition, and mimic catalytic activity. Herein, a capture probe DNA (P1) was immobilized on carboxylated magnetic beads (MBs), allowing for amplified immobilization due to the 3D surface. Subsequently, the presence of the target microRNA-155 led to the formation of a sandwich structure (P2/microRNA-155/P1/MBs) when P2 was introduced to the modified P1/MBs. The HCR reaction was then triggered by adding H1 and H2 to create a super sandwich (H1/H2)n. Following this, Cu2+ ions were attracted to the negatively charged phosphate groups of the (H1/H2)n and reduced by ascorbic acid, resulting in the formation of CuNPs, which were embedded into the grooves of the (H1/H2)n. The peroxidase-like activity of CuNPs catalyzed the oxidation reaction of 3,3',5,5'-Tetramethylbenzidine (TMB), resulting in a distinct blue color measured at 630 nm. Under optimal conditions, the colorimetric biosensor exhibited a linear response to microRNA-155 concentrations ranging from 80 to 500 aM, with a detection limit of 22 aM, and discriminate against other microRNAs. It was also successfully applied to the determination of microRNA-155 levels in spiked human serum.

Robust nontarget DNA-triggered catalytic hairpin assembly amplification strategy for the improved sensing of microRNA in complex biological matrices

A simple but robust fluorescence strategy based on a nontarget DNA-triggered catalytic hairpin assembly (CHA) was constructed to probe microRNA-21 (miR-21). A short ssDNA rather than degradable target miRNA was employed as an initiator. Two molecular beacons needed to assist the CHA process were simplified to avoid unfavorable nonspecific interactions. In the presence of the target, the initiator was released from a partially duplex and triggered the cyclic CHA reaction, resulting in a significantly amplified optical readout. A wide linear range from 0.1 pM to 1000 pM for the sensing of miR-21 in buffer was achieved with a low detection limit of 0.76 pM. Fortunately, this strategy demonstrated an obviously improved performance for miR-21 detection in diluted serum. The fluorescence signals were enhanced remarkably and the sensitivity was further improved to 0.12 pM in 10% serum. The stability for miR-21 quantification and the capability for the analysis of single nucleotide polymorphisms (SNPs) were also improved greatly. More importantly, the biosensor could be applied to image miR-21 in different living tumor cells with high resolution, illustrating its promising potential for the assay of miRNAs in various complex situations for early-stage disease diagnosis and biological studies in cells.

Strategy of functional nucleic acids-mediated isothermal amplification for detection of foodborne microbial contaminants: A review

Foodborne microbial contamination (FMC) is the leading cause of food poisoning and foodborne illness. The foodborne microbial detection methods based on isothermal amplification have high sensitivity and short detection time, and functional nucleic acids (FNAs) could extend the detectable object of isothermal amplification to mycotoxins. Therefore, the strategy of FNAs-mediated isothermal amplification has been emergingly applied in biosensors for foodborne microbial contaminants detection, making biosensors more sensitive with lower cost and less dependent on nanomaterials for signal output. Here, the mechanism of six isothermal amplification technologies and their application in detecting FMC is firstly introduced. Then the strategy of FNAs-mediated isothermal amplification is systematically discussed from perspectives of FNAs' versatility including recognition elements (Aptamer, DNAzyme), programming tools (DNA tweezer, DNA walker and CRISPR-Cas) and signal units (G-quadruplex, FNAs-based nanomaterials). Finally, challenges and prospects are presented in terms of addressing the issue of nonspecific amplification reaction, developing better FNAs-based sensing elements and eliminating food matrix effects.

Programmable electrochemical biosensing platform based on catalytic hairpin assembly and entropy-driven catalytic cascade amplification circuit

Herein, powerful DNA strand displacement reaction and sensitive electrochemical analysis method were ingeniously integrated to develop a programmable biosensing platform. Using DNA as the detection model, a cascade amplification system based on catalytic hairpin assembly and entropy-driven catalytic was constructed, and the reaction rate and signal amplification effect were significantly improved. The product of the cascade amplification circuit could undergo strand displacement reaction with the signal probe on the electrode surface to obtain sensitive electrochemical signal changes and realize highly sensitive detection of the target. In addition, without redesigning the DNA sequences in the cascade amplification circuit, the by-product strand typically wasted in traditional entropy-driven catalytic reactions can be fully utilized to construct a single-signal output biosensing system and even a dual-signal output ratiometric biosensing platform, improving the detection repeatability and reliability of the system, and expanding the application of DNA strand displacement reaction in electrochemical biosensing. Furthermore, benefiting from the design flexibility of the DNA molecules, the constructed biosensing platform realized the sensitive detection of aptamer substrate (kanamycin as an example) and certain metal ion (mercury as an example) by simply recoding the corresponding recognition sequence, demonstrating the good versatility of the biosensing platform.

A Cascade Signal Amplification Strategy for the Ultrasensitive Fluorescence Detection of Cu2+ via λ-Exonuclease-Assisted Target Recycling with Mismatched Catalytic Hairpin Assembly

Herein, an ultrasensitive DNAzyme-based fluorescence biosensor for detecting Cu2+ was designed using the cascade signal amplification strategy, coupling λ-exonuclease-assisted target recycling and mismatched catalytic hairpin assembly (MCHA). In the designed detection system, the target, Cu2+, can activate the Cu2+-dependent DNAzyme to cause a cleavage reaction, releasing ssDNA (tDNA). Then, tDNA binds to hairpin DNA (H0) with an overhanging 5'-phosphorylated terminus to form dsDNA with a blunt 5'-phosphorylated terminus, which activates the dsDNA to be digested by λ-Exo and releases tDNA along with another ssDNA (iDNA). Subsequently, the iDNA initiates MCHA, which can restore the fluorescence of carboxyfluorescein (FAM) previously quenched by tetramethylrhodamine (TAMRA), resulting in a strong fluorescent signal. Furthermore, MCHA efficiently improves the signal-to-noise ratio of the detection system. More importantly, tDNA recycling can be achieved with the λ-Exo digestion reaction to release more iDNA, efficiently amplifying the fluorescent signal and further improving the sensitivity to Cu2+ with a detection limit of 60 fM. The practical application of the developed biosensor was also demonstrated by detecting Cu2+ in real samples, proving it to be an excellent analytical strategy for the ultrasensitive quantification of heavy metal ions in environmental water sources.

Integration of Isothermal Enzyme-Free Nucleic Acid Circuits for High-Performance Biosensing Applications

The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed.

Bio-barcode assay: A useful technology for ultrasensitive and logic-controlled specific detection in food safety: A review

Food safety is one of the greatest public health challenges. Developing ultrasensitive detection methods for analytes at ultra-trace levels is, therefore, essential. In recent years, the bio-barcode assay (BCA) has emerged as an effective ultrasensitive detection strategy that is based on the indirect amplification of various DNA probes. This review systematically summarizes the progress of fluorescence, PCR, and colorimetry-based BCA methods for the detection of various contaminants, including pathogenic bacteria, toxins, pesticides, antibiotics, and other chemical substances in food in over 120 research papers. Current challenges, including long experimental times and strict storage conditions, and the prospects for the application of BCA in biomedicine and environmental analyses, have also been discussed herein.

Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection

Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.

Visualized Lateral Flow Assay for Dual Viral RNA Fragment Detection

In this technical note, we report an easy-to-produce, reverse-transcription-free, and protein-enzyme-free lateral flow assay for detection of viral RNA fragments by taking SARS-CoV-2 ORF1ab and N as target models. Catalytic hairpin assembly is utilized for dual RNA fragment orthogonal reaction to generate copious amounts of opened hairpin duplexes, which bridge DNA-modified gold nanoparticles and capture strands on the strip to induce coloration. The dual RNA fragments are simultaneously visualized during one time of sample flow, and single-base-mismatched nontarget sequences can be differentiated. The test strip can be flexibly adapted to detect evolutional SARS-CoV-2 variants such as Delta and Omicron. It also shows potential in visually detecting long-sequence virus simulants and achieves a sensitivity comparable to that of RT-qPCR by incorporation with upstream sample amplification. The lateral flow assay should offer a convenient and reliable technique for viral nucleic acid detection.

A ratiometric fluorescence platform for lead ion detection via RNA cleavage-inhibited self-assembly of three-arm branched junction

Heavy metal pollution can pose a threat to food safety and human health, and accurate quantification of heavy metal ions is a vital requirement. Emerging DNA nanostructures-based biosensors offer attractive tools toward ultra-sensitive or rapid analysis of heavy metal ions. However, the problems including complex design, severe reaction conditions and undesirable reliability are inevitable obstacle in advancing their extension and application. Herein, a ratiometric fluorescent platform was established for monitoring lead ion (Pb²⁺) in food based on dual Förster resonance energy transfer (FRET) and RNA cleavage-inhibited self-assembly of three-arm branched junction (TBJ). GR-5 DNAzyme was employed for Pb²⁺ recognition, and enzyme-free amplification technique catalytic hairpin assembly (CHA) served to form FRET probes-carried TBJ. The substrate strand (S) of DNAzyme triggered the generation of CHA-TBJ, and Pb²⁺-responsive cleavage of S hindered the assembly of CHA-TBJ, causing opposite changes in the FRET states of FAM/BHQ1 and ROX/BHQ2 pairs. The fluorescence responses were recorded through synchronous fluorescence spectrometry to indicate Pb²⁺ concentration, allowing sensitive and reliable identification of Pb²⁺ in the linear range of 0.05-5 ng mL^-1 with the detection limit of 0.03 ng mL^-1. The Pb²⁺ detection can be achieved under conventional reaction conditions, simple mixing procedures and one-step measurement operation. The approach can afford excellent specificity for Pb²⁺ against competing metal ions, and can be applied to analyze Pb²⁺ in tea samples with satisfactory results. This facile fluorescence platform shows a capable method for Pb²⁺ detection, and provides new avenue in the development of ratiometric approaches and DNAzyme strategies for monitoring heavy metal pollution, facilitating the transformation of DNAzyme-based biosensors for food safety control.

Accurate and rapid quantification of PD-L1 positive exosomes by a triple-helix molecular probe

Programmed death ligand-1 (PD-L1) positive exosomes (P-Exo) have been widely used for tumor diagnosis. However, accurate and rapid quantification of P-Exo remains challenging due to the heterogeneity of clinical individuals and isolation techniques. In this study, the triple-helix molecular probe (THMP) coupled with high-affinity silica-based TiO₂ magnetic beads was used to isolate exosomes and to analyze the relative abundance of P-Exo in total exosomes (T-Exo). By employing this strategy, the entire analysis was completed within 70 min and the detection limit for P-Exo was 880 particles μL^-1. Additionally, the relative abundance of P-Exo in T-Exo (RA_P-Exo/T-Exo) was calculated from their fluorescence ratio, which could avoid errors due to differences in samples and separation methods, and identify 1.5 × 10³ P-Exo from 5 × 10⁶ T-Exo per microliter. RA_P-Exo/T-Exo values were not only effective in distinguishing healthy volunteers from breast cancer patients, but also highly positively correlated with the stage of breast carcinoma. Overall, this strategy opens a new avenue for rapid and quantitative analysis of P-Exo, providing an opportunity for precise diagnosis and prediction of treatment efficacy in cancer.

Cascade DNA Circuits Mediated CRISPR-Cas12a Fluorescent Aptasensor based on Multifunctional Fe3 O4 @hollow-TiO2 @MoS2 Nanochains for Tetracycline Determination

Herein, for the first time, the CRISPR-Cas12a system is combined with aptamer, cascaded dynamic DNA network circuits, and Fe₃ O₄ @hollow-TiO₂ @MoS₂ nanochains (Fe₃ O₄ @h-TiO₂ @MoS₂ NCs) to construct an efficient sensing platform for tetracycline (TC) analysis. In this strategy, specific recognition of the target is transduced and amplified into H1-H2 duplexes containing the specific sequence of Cas12a-crRNA through an aptamer recognition module and the dual amplification dynamic DNA network. Subsequently, the obtained activated Cas12a protein non-specifically cleaves the adjacent reporter gene ssDNA-FAM to dissociate the FAM molecule from the quencher Fe₃ O₄ @h-TiO₂ @MoS₂ NCs, resulting in the recovery of the fluorescence signal and further signal amplification. Particularly, the synthesized multifunctional Fe₃ O₄ @h-TiO₂ @MoS₂ NCs composites also exhibit superb magnetic separability and photocatalytic degradation ability. Under optimal conditions, the aptasensor displays a distinct linear relationship with the logarithm of TC concentration, and the limit of detection is as low as 0.384 pg mL^-1 . Furthermore, the results of spiked recovery confirm the viability of the proposed aptasensor for TC quantification in real samples. This study extends the application of the CRISPR-Cas12a system in the field of analytical sensing and contributes new insights into the exploration of reliable tools for monitoring and treating hazards in food and environment.

Dual-target nucleic acid sequences responsive electrochemiluminescence biosensor using single type carbon dots as probe for SARS-CoV-2 detection based on series catalytic hairpin assembly amplification

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is rampant all over the world, and rapid and effective virus detection is the best auxiliary to curb the spread of the epidemic. A diagnosis can only be made if two or more different nucleic acid sequences are confirmed at the same time, and in most of traditional detection technologies, these target sequences have been detected separately. In this work, an electrochemiluminescent (ECL) biosensor employing a single ECL probe as signal output and responding to dual-target simultaneously is proposed for the first time. Taking the two sequences located in ORF 1ab region and N region of SARS-CoV-2 gene sequence as the model target and nitrogen doped carbon quantum dots (CDs) as ECL beacon, supplemented with catalytic hairpin assembly (CHA) reaction for signal amplification, the presented strategy has been successfully applied to the rapid detection of SARS-CoV-2. The developed SARS-CoV-2 biosensor based on the series CHA systems can realize the quantitative determination of SARS-CoV-2 in the range of 50 fM to 200 pM within 40 min. Moreover, the clinical validity of this method has been verified by the high consistency between the detection results of using this method and those using RT-qPCR for seven clinical pharyngeal swab samples.