Target-triggered entropy-driven amplification system-templated silver nanoclusters for multiplexed microRNA analysis

Functional DNA-Zn2+ coordination nanospheres for sensitive imaging of 8-oxyguanine DNA glycosylase activity in living cells

Sensitive monitoring of human 8-oxyguanine DNA glycosylase (hOGG1) activity in living cells is helpful to understand its function in damage repair and evaluate its role in disease diagnosis. Herein, a functional DNA-Zn2+ coordination nanospheres was proposed for sensitive imaging of hOGG1 in living cells. The nanospheres were constructed through the coordination-driven self-assembly of the entropy driven reaction (EDR) -deoxyribozyme (DNAzyme) system with Zn2+, where DNAzyme was designed to split structure and assembled into the EDR system. When the nanospheres entered the cell, the competitive coordination between phosphate in the cell and Zn2+ leaded to the disintegration of the nanospheres, releasing DNA and some Zn2+. The released Zn2+ acted as a cofactor of DNAzyme. In the presence of hOGG1, the EDR was completed, accompanied by fluorescence recovery and the generation of a complete DNAzyme. With the assistance of Zn2+, DNAzyme continuously cleaved substrates to produce plenty of fluorescence signals, thus achieving sensitive imaging of hOGG1 activity. The nanospheres successfully achieved sensitive imaging of hOGG1 in human cervical cancer cells (HeLa), human non-small cell lung cancer cells and human normal colonic epithelial cells, and assayed changes in hOGG1 activity in HeLa cells. This nanospheres may provide a new tool for intracellular hOGG1 imaging and related biomedical studies.

Detection of MicroRNA-155 based on lambda exonuclease selective digestion and CRISPR/cas12a-assisted amplification

In numerous malignancies, miRNA-155 is overexpressed and has oncogenic activity because it is one of the most efficient microRNAs for inhibiting apoptosis in human cancer cells. As a result, the highest sensitive detection of the miRNA-155 gene is a technological instrument that can enable early cancer screening. In this study, a miRNA-155 biosensor was created to create a hairpin probe that can bind to the miRNA-155 gene using lambda nucleic acid exonuclease, which can cut the 5' phosphorylated double strand, and by the DNA probe is recognized by the Cas12a enzyme, which then activates Cas12a to catalyze trans-cutting produces strong fluorescence. Research finding, the target concentration's logarithm and corresponding fluorescence intensity have a strong linear connection, and the limit of detection (LOD) of the sensing system was determined to be 8.3 pM. In addition, the biosensor displayed exceptional specificity, low false-positive signal, and high sensitivity in detecting the miRNA-155 gene in serum samples. This study's creation of a biosensor that has high sensitivity, good selectivity, and is simple to operate provides promising opportunities for research into biosensor design and early cancer detection.

Dual amplification dynamic DNA network system for CRISPR/Cas12a based p53 gene detection

BACKGROUND

It is estimated that over 50 % of human cancers are caused by mutations in the p53 gene. Early sensitive and accurate detection of the p53 gene is important for diagnosis of cancers in the early stage. However, conventional detection techniques often suffer from strict reaction conditions, or unsatisfied sensitivity, so we need to develop a new strategy for accurate detection of p53 gene with smart designability, multiple signal amplification in mild reaction conditions.

RESULTS

In this study, CRISPR/Cas system is exploited in entropy-driven catalysis (EDC) and hybridization chain reaction (CHA) dual signal amplification sensing strategies. The products of both reactions can efficiently and separately activate CRISPR/Cas12a which greatly amplifies the fluorescent signal. The method has good linearity in p53 detection with the concentration ranged from 0.1 fM to 0.5 pM with ultra-low detection limit of 0.096 fM. It also showed good performance in serum, offering potentials for early disease detection.

SIGNIFICANCE

The designed dual amplification dynamic DNA network system exhibits an ultra-sensitive fluorescence biosensing for p53 gene identification. The method is simple to operate and requires only one buffer for the experiment, and meanwhile shows smart designability which could be used for a wide range of markers. Thus, we believe the present work will provide a potential tool for the construction and development of sensitive fluorescent biosensors for diseases.

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.

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.

Triplex DNA-based aggregation-induced emission probe: A new platform for hybridization chain reaction-based fluorescence sensing assay

The hybridization chain reaction (HCR), as one of the nucleic acid amplification technologies, is combined with fluorescence signal output with excellent sensitivity, simplicity, and stability. However, current HCR-based fluorescence sensing methods still have some defects such as the blocking effect of the HCR combination with fluorophores and the aggregation-caused quenching (ACQ) phenomenon of traditional fluorophores. Herein, a triplex DNA-based aggregation-induced emission probe (AIE-P) was designed as the fluorescent signal transduction, which is able to provide a new platform for HCR-based sensing assay. The AIE-P was synthesized by attaching the AIE fluorophores to terminus of the oligonucleotide through amido bond, and captured the products of HCR to form triplex DNA. In this case, the AIE fluorophores were located in close proximity to generate fluorescence. This assay provided turn-on fluorescence efficiency with a high signal-to-noise ratio and excellent amplification capability to solve the shortcoming of HCR-based fluorescence sensing methods. It enabled sensitive detection of Vibrio parahaemolyticus in the range of 102-106 CFU mL-1, and with a low limit of detection down to 39 CFU mL-1. In addition, this assay expressed good specificity and practicability. The triplex DNA-based AIE probe forms a universal molecular tool for developing HCR-based fluorescence sensing methods.

Fluorescence Biosensing Based on Bifurcated DNA Scaffold-Aggregated Ag Nanocluster via Responsive Conformation Switch of Quasi-Molecular Beacon

To address the limitations of typical hairpin-structural molecular beacons, exploring the ability of a quasi-molecular beacon (qMB) to create label-free fluorescence biosensors is intriguing and remains a challenge. Herein, we propose the first example of modular qMB with the feature of a stimulation-responsive conformation switch to develop an aggregated Ag nanocluster (aAgNC) in a bifurcated DNA scaffold for fluorescently sensing a specific initiator (I*). This qMB was well designed to program four functional modules: I*-recognizable element adopting metastable stem-loop bihairpin structure and two DNA splits (exposed C3GT4 and locked C4AC4T) of aAgNC template that is separated by a tunable hairpin spacer for the customized combination of selective recognition and signaling readout. When presenting I* in an assay route, the specific hybridization induces the directional disassembly of the bihairpin unit, on which the qMB is configurationally switched to liberate the locked split. Thus, the bifurcated parent template pair of C3GT4/C4AC4T is proximal, affording in situ nucleation and clustering of emissive aAgNC. By collecting the fluorescence signal, the quantitative detection of I* is achieved. Benefiting from the ingenious programming of qMB, the recognizing and signaling integration actuates the construction of a facile and convenient fluorescent biosensor featuring rapid reaction kinetics, a wide linear range, high sensitivity, and specificity. This would provide a new paradigm to exploit versatile qMB-based biosensing platforms via stimulation-responsive conformation switches for developing various DNA-scaffolded Ag clusters.

Multiplex Detection of Single Nucleotide Polymorphisms by Liquid Chromatography for Nonsmall Cell Lung Cancer Staging

In this work, an integrated strategy with excellent accuracy and high throughput is proposed for the precise indication of single nucleotide polymorphism (SNP) in nonsmall cell lung cancer diseases. Two types of point mutations (L858R and T790M) and the corresponding wild types could be identified together in a single high-performance liquid chromatographic run. Signal amplification was achieved through a series of enzyme ligation, primer extension, and enzyme cleavage strategies, and a large number of DNA probes with different fluorescence signals were finally generated. The factors affecting the spatiotemporal separation efficiency of four DNA probes were systematically investigated. The limits of detection of wild types (WTs) or mutant types (MTs) abbreviated as L858R-MT, L858R-WT, T790M-MT, and T790M-WT were 26, 24, 19, and 22 aM, respectively. In addition, the levels of mutant types and wild types in the serum of 40 nonsmall cell lung cancer patients at different stages were detected using the method, and the correlation between the mutation ratios and cancer stages was preliminarily verified. The proposed highly selective and sensitive method may serve as an alternative approach for early diagnosis and staging of nonsmall cell lung cancer.

A cascade signal-amplified fluorescent biosensor combining APE1 enzyme cleavage-assisted target cycling with rolling circle amplification

A cascade signal-amplified fluorescent biosensor was developed for miRNA-21 detection by combining APE1 enzyme-assisted target recycling and rolling circle amplification strategy. A key feature of this biosensor is its dual-trigger mechanism, utilizing both tumor-endogenous miRNA-21 and the APE1 enzyme in the initial amplification step, followed by a second rolling circle amplification reaction. This dual signal amplification cascade significantly enhanced sensitivity, achieving a detection limit of 3.33 pM. Furthermore, this biosensor exhibited excellent specificity and resistance to interference, allowing it to effectively distinguish and detect the target miRNA-21 in the presence of multiple interfering miRNAs. Moreover, the biosensor maintained its robust detection capabilities in a 10% serum environment, demonstrating its potential for clinical disease diagnosis applications.

Label-Free, High-Throughput, Sensitive, and Logical Analysis Using Biomimetic Array Based on Stable Luminescent Copper Nanoclusters and Entropy-Driven Nanomachine

The development of an array for high-throughput and logical analysis of biomarkers is significant for disease diagnosis. DNA-templated copper nanoclusters (CuNCs) have a strong potential to serve as a label-free photoluminescence source in array platforms, but their luminescent stability and sensitivity need to be improved. Herein, we report a facile, sensitive, and robust biomimetic array assay by integrating with stable luminescent CuNCs and entropy-driven nanomachine (EDN). In this strategy, the luminescent stability of CuNCs was improved by adding fructose in CuNCs synthesis to offer a reliable label-free signal. Meanwhile, the DNA template for CuNCs synthesis was introduced into EDN with excellent signal amplification ability, in which the reaction triggered by target miRNA would cause the blunt/protruding conformation change of 3'-terminus accompanied by the production or loss of luminescence. In addition, a biomimetic array fabricated by photonic crystals (PCs) physically enhanced the emitted luminescent signal of CuNCs and achieved high-throughput signal readout by a microplate reader. The proposed assay can isothermally detect as low as 4.5 pM of miR-21. Moreover, the logical EDN was constructed to achieve logical analysis of multiple miRNAs by "AND" or "OR" logic gate operation. Therefore, the proposed assay has the advantages of label-free property, high sensitivity, flexible design, and high-throughput analysis, which provides ideas for developing a new generation of facile and smart platforms in the fields of biological analysis and clinical application.

Dual-Signal Cascaded Nucleic Acid Amplification Circuit-Loaded Metal-Organic Frameworks for Accurate and Robust Imaging of Intracellular MicroRNA

Cascaded signal amplification technologies play an important role in the sensitive detection of lowly expressed biomarkers of interests yet are constrained by severe background interference and low cellular accessibility. Herein, we constructed a metal-organic framework-encapsulating dual-signal cascaded nucleic acid sensor for precise intracellular miRNA imaging. ZIF-8 nanoparticles load and deliver FAM-labeled upstream catalytic hairpin assembly (CHA) and Cy5-modified downstream hybridization chain reaction (HCR) hairpin reactants to tumor cells, enabling visualization of the target-initiated signal amplification process for double-insurance detection of analytes. The pH-responsive ZIF-8 nanoparticles effectively protect DNA hairpins from degradation and allow the release of them in the acid tumor microenvironment. Then, intracellular target miRNAs orderly trigger cascaded nucleic acid signal amplification reaction, of which the exact progress is investigated through the analysis of the fluorescence recovering process of FAM and Cy5. In addition, DNA@ZIF-8 nanoparticles improve measurement accuracy by dual-signal colocalization imaging, effectively avoiding nonspecific false-positive signals and enabling in situ imaging of miRNAs in living cells. A dual-signal colocalization strategy allows accurate target detection in living cells, and DNA@ZIF-8 provides a promising intracellular sensing platform for signal amplification and visual monitoring.

Simultaneous detection and imaging of two specific miRNAs using DNA tetrahedron-based catalytic hairpin assembly

Improving the accuracy, sensitivity and speed of intracellular miRNA imaging is essential for early diagnosis of cancer. To achieve this goal, we herein present a strategy for imaging two distinct miRNAs by DNA tetrahedron-based catalytic hairpin assembly (DCHA). Two nanoprobes, DTH-13 and DTH-24, were prepared by one-pot synthesis. The resultant structures were DNA tetrahedrons functionalized with two sets of CHA hairpins, which respectively responded to miR-21 and miR-155. Using these structured DNA nanoparticles as the carriers, the probes could easily enter living cells. The presence of miR-21 or miR-155 could trigger CHA between DTH-13 and DTH-24, leading to independent fluorescence signals of FAM and Cy3. In this system, the sensitivity and kinetics were significantly enhanced owing to the strategy of DCHA. The sensing performance of our method was thoroughly investigated in buffers, fetal bovine serum (FBS) solutions, living cells, and clinical tissue samples. The results validated the potential of DTH nanoprobes as a diagnostic tool for early stages of cancer.

Application of Metal-Based Nanomaterials in In Vitro Diagnosis of Tumor Markers: Summary and Prospect

Cancer, which presents with high incidence and mortality rates, has become a significant health threat worldwide. However, there is currently no effective solution for rapid screening and high-quality treatment of early-stage cancer patients. Metal-based nanoparticles (MNPs), as a new type of compound with stable properties, convenient synthesis, high efficiency, and few adverse reactions, have become highly competitive tools for early cancer diagnosis. Nevertheless, challenges such as the difference between the microenvironment of detected markers and the real-life body fluids remain in achieving widespread clinical application of MNPs. This review provides a comprehensive review of the research progress made in the field of in vitro cancer diagnosis using metal-based nanoparticles. By delving into the characteristics and advantages of these materials, this paper aims to inspire and guide researchers towards fully exploiting the potential of metal-based nanoparticles in the early diagnosis and treatment of cancer.

Modular Engineering of a DNA Tetrahedron-Based Nanomachine for Ultrasensitive Detection of Intracellular Bioactive Small Molecules

Bioactive small molecules serve as invaluable biomarkers for recognizing modulated organismal metabolism in correlation with numerous diseases. Therefore, sensitive and specific molecular biosensing and imaging in vitro and in vivo are particularly critical for the diagnosis and treatment of a large group of diseases. Herein, a modular DNA tetrahedron-based nanomachine was engineered for the ultrasensitive detection of intracellular small molecules. The nanomachine was composed of three self-assembled modules: an aptamer for target recognition, an entropy-driven unit for signal reporting, and a tetrahedral oligonucleotide for the transportation of the cargo (e.g., the nanomachine and fluorescent markers). Adenosine triphosphate (ATP) was used as the molecular model. Once the target ATP bonded with the aptamer module, an initiator was released from the aptamer module to activate the entropy-driven module, ultimately activating the ATP-responsive signal output and subsequent signal amplification. The performance of the nanomachine was validated by delivering it to living cells with the aid of the tetrahedral module to demonstrate the possibility of executing intracellular ATP imaging. This innovative nanomachine displays a linear response to ATP in the 1 pM to 10 nM concentration range and demonstrates high sensitivity with a low detection limit of 0.40 pM. Remarkably, our nanomachine successfully executes endogenous ATP imaging and is able to distinguish tumor cells from normal ones based on the ATP level. Overall, the proposed strategy opens up a promising avenue for bioactive small molecule-based detection/diagnostic assays.

Nanoarchitectonics-Assisted Simultaneous Fluorescence Detection of Urinary Dual miRNAs for Noninvasive Diagnosis of Prostate Cancer

Herein, we report a fluorescence strategy for the homogeneous and simultaneous analysis of urine miRNA-375 and miRNA-148a. The target miRNAs in urine bonded the devised dumbbell-shaped "C-Ag⁺-C" and "T-Hg²⁺-T" hairpin structures that could trigger cascade enzyme-free amplification. Then, the fluorescent CdTe quantum dots (QDs) and carbon dots (CDs) could selectively recognize Ag⁺ and Hg²⁺, to quantify the dual miRNAs concurrently. Under optimized conditions, the linear range was from 0.1 to 1000 fM and the limits of detection (LOD) for dual miRNAs reached 30 and 25 aM, respectively. The practicality was further evaluated with 45 clinical urine samples including prostate cancer (PC) and other patients, and the results were consistent with the clinical polymerase chain reaction (PCR) kit and ultrasonic and pathological findings. The receiver operating characteristic (ROC) curve analysis showed that the estimates of the area under the curve (AUC) were 0.739 for the serum prostate-specific antigen (PSA) and 0.941 for miRNA-375 and 0.946 for miRNA-148a. The sensitivity and specificity reached 75 and 100% for miRNA-375 and 71 and 94% for miRNA-148a, respectively, which was better than serum PSA. This strategy constructed a reliable system for dual miRNA detection in urine samples and proposed new insights into the rapid and noninvasive diagnosis of PC.

Nucleic Acid Amplification by Template-Dominated Click Chemistry for Ultrasensitive DNA/RNA Detection on an Electrochemical Readout Platform

As an enzyme-free exponential nucleic acid amplification method, the click chemistry-mediated ligation chain reaction (ccLCR) has shown great prospects in the molecular diagnosis. However, the current optics-based ccLCR is challenged by remarkable nonspecific amplification, severely hindering its future application. This study demonstrated that the severe nonspecific amplification was generated probably due to high random collision in the high DNA probe concentration (μM level). To solve this hurdle, a nucleic acid template-dominated ccLCR was constructed using nM-level DNA probes and read on an electrochemical platform (cc-eLCR). Under the optimal conditions, the proposed cc-eLCR detected a low-level nucleic acid target (1 fM) with a single-base resolution. Furthermore, this assay was applied to detect the target of interest in cell extracts with a satisfactory result. The proposed cc-eLCR offers huge possibility for click chemistry-mediated enzyme-free exponential nucleic acid amplification in the application of medical diagnosis and biomedical research.

An enzyme-powered microRNA discriminator for the subtype-specific diagnosis of breast cancer

Breast cancer, a disease with highly heterogeneous features, is the most common malignancy diagnosed in people worldwide. Early diagnosis of breast cancer is crucial for improving its cure rate, and accurate classification of the subtype-specific features is essential to precisely treat the disease. An enzyme-powered microRNA (miRNA, RNA = ribonucleic acid) discriminator was developed to selectively distinguish breast cancer cells from normal cells and further identify subtype-specific features. Specifically, miR-21 was used as a universal biomarker to discriminate between breast cancer cells and normal cells, and miR-210 was used to identify triple-negative subtype features. The experimental results demonstrated that the enzyme-powered miRNA discriminator displayed low limits of detection at fM levels for both miR-21 and miR-210. Moreover, the miRNA discriminator enabled the discrimination and quantitative determination of breast cancer cells derived from different subtypes based on their miR-21 levels, and the further identification of the triple-negative subtype in combination with the miR-210 levels. Therefore, it is hoped that this study will provide insight into subtype-specific miRNA profiling, which may have potential use in the clinical management of breast tumours based on their subtype characteristics.

Redox-labelled detection probe enabled immunoassay for simultaneous detection of multiple cancer biomarkers

Some of the cancer biomarkers often lack specificity and sensitivity; thus, simultaneous detection of multiple biomarkers can make the diagnosis more accurate. Also, simple sensing system without utilization of extra reagents like mediator or substrate during detection event is desirable for point-of-care testing. To address this, mediator and substrate-free amperometric biosensor for simultaneous detection of cancer biomarkers carcinoembryonic antigen (CEA) and alpha-fetoprotein (AFP) have been demonstrated by designing two different redox-labelled detection probes. Colloidal nanoparticles of polyaniline-pectin conjugated with AFP antibody along with ferrocene and silver nanoparticles conjugated with CEA antibody along with anthraquinone were used as redox probes to bind with AFP and CEA during the detection event. Sensor constructed using carboxylic acid tethered polyaniline as immobilization matrix displayed 5 times wider linear range than conventional polyaniline for AFP and CEA detection by sandwich electrochemical assay. The detection limit was 30 pg mL^-1 for AFP and 80 pg mL^-1 for CEA. The biosensor displayed appropriate sensitivity, good specificity, and negligible cross-reactivity between the two targets. The proposed sensor was used to determine APF and CEA in human blood serum. The strategy demonstrated can be further extended for detection of panel of cancer biomarkers by designing appropriate redox probes.

A novel DNA detection using spherical identification probe and strand displacement reaction-initiated silver nanocluster switch

Herein, we developed a novel fluorescent assay using spherical identification probes and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch. In this strategy, the target was captured by the spherical probes to induce the activity of exonuclease III (Exo III), catalyzing the cyclic cleavage of substrates to produce a mass of trigger strands. After magnetic bead separation, the intermediates in the supernatant activated downstream toehold-mediated strand displacement reaction to change the structure of silver nanocluster templates, leading to fluorescence intensity reduction. Furthermore, it is demonstrated that the application of spherical identification probes could reduce the signal leakage and the limit of detection. In addition, AgNCs with perfect optical property were ingeniously combined to realize signal output, which reduced the cost and time of synthesis. Under the optimal conditions, the sensing method displayed a good linear range from 250 pM to 25 nM with a detectable minimum concentration of 250 pM. And the practical application potential in complex biological matrices was also evaluated. Considering these advantages, this constructed strategy opens a new path for nucleic acid detection with better performance. A simple, label- and hairpin-free fluorescent system based on spherical identification probe and toehold-mediated strand displacement reaction-initiated silver nanoclusters (AgNCs) "on-off" signal switch was successfully constructed to detect target DNA.

Protein-free, ultrasensitive miRNA analysis based on an entropy-driven catalytic reaction switched on a smart-responsive DNAzyme dual-walker amplification strategy

MicroRNAs (miRNAs), useful biomarkers for cancer diagnosis, play an important role in tumorigenesis and progression, but many of the current analysis methods can suffer from excessive protease dependence, being time-consuming and unsatisfactory performance. Therefore, a reliable sensing strategy for the protein-free, ultrasensitive analysis of tumor-associated miRNAs is desired. The proposed dual-walker biosensing strategy based on an entropy-driven catalytic (EDC) walker coupled with a smart-responsive DNAzyme walker was demonstrated for the dual-amplification detection of miRNA-21. Namely, the target miRNA-21 initiates the three-stranded substrate complex of the traditional EDC circuit to release the input trigger of the Dz walker, which recognizes the circular binding domain to restore the cleavage activity of the DzS-AuNP walker. The fluorescence signal continuously released from the AuNPs was recorded by a fluorescence reader for miRNA-21 sensing. The optimized dual-walker exhibited appreciable sensitivity with a detection limit of 70 fM, satisfactory flexibility, fine specificity and ideal stability for clinical serum sample assays. The proposed strategy may open a new avenue for the development of powerful DNA molecular tools for cancer diagnosis.

Nucleic acid amplification-based strategy to detect foodborne pathogens in milk: a review

Milk contaminated with trace amounts of foodborne pathogens can considerably threaten food safety and public health. Therefore, rapid and accurate detection techniques for foodborne pathogens in milk are essential. Nucleic acid amplification (NAA)-based strategies are widely used to detect foodborne pathogens in milk. This review article covers the mechanisms of the NAA-based detection of foodborne pathogens in milk, including polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), rolling circle amplification (RCA), and enzyme-free amplification, among others. Key factors affecting detection efficiency and the advantages and disadvantages of the above techniques are analyzed. Potential on-site detection tools based on NAA are outlined. We found that NAA-based strategies were effective in detecting foodborne pathogens in milk. Among them, PCR was the most reliable. LAMP showed high specificity, whereas RPA and RCA were most suitable for on-site and in-situ detection, respectively, and enzyme-free amplification was more economical. However, factors such as sample separation, nucleic acid target conversion, and signal transduction affected efficiency of NAA-based strategies. The lack of simple and effective sample separation methods to reduce the effect of milk matrices on detection efficiency was noteworthy. Further research should focus on simplifying, integrating, and miniaturizing microfluidic on-site detection platforms.

Simple Amplifier Coupled with a Lanthanide Labeling Strategy for Multiplexed and Specific Quantification of MicroRNAs

Inductively coupled plasma-mass spectrometry (ICP-MS) with elemental labeling is a promising strategy for multiplex microRNA (miRNA) analysis. However, it is still challenging for specific analysis of multiple miRNAs with high homology, and the development of multiplex assays is always limited by the complexity of the sequence design. Herein, a simple and direct ICP-MS-based assay was developed for the simultaneous detection of three miRNAs by combining the lanthanide labeling strategy with entropy-driven catalytic (EDC) amplification. Owing to the specificity of EDC for nucleic acid recognition, it is able to differentiate miRNAs with single-base mutation in each EDC circuit. A universal biotin-labeled DNA strand was designed to hybridize with the DNA substrates for three EDC circuits, targeting miRNA-21, miRNA-155, and miRNA-10b, respectively. All the substrates were loaded on the surface of streptavidin magnetic beads. In the presence of target miRNA, the EDC reaction was initiated, and EDC substrates were dissociated, continuously releasing reporter strands that were labeled with lanthanides (Tb/Ho/Lu). After magnetic separation, the supernatant containing the released reporter strands was introduced into an ICP-MS system for simultaneous detection of ¹⁵⁹Tb/¹⁶⁵Ho/¹⁷⁵Lu and quantification of miRNA-21, miRNA-155, and miRNA-10b, respectively. The limits of detection were 7.4, 7.5, and 11 pmol L^-1 for miRNA-21, miRNA-155, and miRNA-10b, respectively. Overall, this study provides a powerful strategy for simultaneous quantification of multiple miRNAs, with the advantages of flexible probe design, good sensitivity, and excellent specificity.

Development of Enzyme-Free DNA Amplifier Based on Chain Reaction Principle

Enzyme-free DNA amplifiers can amplify the signal of nucleic acid molecules. They can be applied to DNA molecular operation and nucleic acid detection. The reaction speed is the core index to evaluate DNA amplifiers. In this study, we designed a DNA amplifier based on an enzyme-free chain reaction. This DNA amplifier can release one more signal molecule in each round of reaction and trigger the next round, which significantly improved reaction speed. Moreover, because the amplifier used a stable DNA structure, the reaction can occur at room temperature. To integrate the amplifier into other DNA molecular operations, we performed the amplification reaction in a microfluidic chip module. The results showed that the amplifier can realize real-time signal feedback at a proper input molecule concentration and reach the endpoint in 40 s, even at a low relative concentration. To apply the amplifier for nucleic acid detection, we also used a conventional fluorescent polymerase chain reaction instrument for the reaction. The results showed that the amplifier specifically detected trace DNA single-stranded molecules. To solve the leakage problem of existing amplifiers, we designed a DNA molecule as the chain reaction's inhibitor, which was crucial in controlling the reaction speed and preventing leakage. STATEMENT OF SIGNIFICANCE: Traditional amplifier strategies of enzyme-free DNA amplifiers relied on a constant number of cycling molecules to catalyze the amplifier molecules' changing structure and release fluorescent signals, which lead low reaction speed. Based on an enzyme-free chain reaction, we designed a DNA amplifier which can release one more cycling molecule in each loop and trigger the next loop and significantly improve reaction speed in this study. Our analysis on microfluidic chip module and PCR instrument verifies high sensitivity and selectivity. And this strategy of DNA amplifier realizes the control of reaction and prevents leakage. We believe that this automated amplification strategy could have great applications in vivo signal detection, imaging, and signal molecule translation.

Label-Free miRNA-21 Analysis Based on Strand Displacement and Terminal Deoxynucleotidyl Transferase-Assisted Amplification Strategy

MicroRNAs (miRNAs) are regarded as a rising star in the biomedical industry. By monitoring slight increases in miRNA-21 levels, the possibilities of multi-type malignancy can be evaluated more precisely and earlier. However, the inconvenience and insensitivity of traditional methods for detecting miRNA-21 levels remains challenging. In this study, a partially complementary cDNA probe was designed to detect miRNA-21 with target-triggered dual amplification based on strand displacement amplification (SDA) and terminal deoxynucleotidyl transferase (TdT)-assisted amplification. In this system, the presence of miRNA-21 can hybridize with template DNA to initiate SDA, generating a large number of trigger molecules. With the assistance of TdT and dGTP, the released trigger DNA with 3′-OH terminal can be elongated to a superlong poly(guanine) sequence, and a notable fluorescence signal was observed in the presence of thioflavin T. By means of dual amplification strategy, the sensing platform showed a good response tomiRNA-21 with a detection limit of 1.7 pM (S/N = 3). Moreover, the specificity of this method was verified using a set of miRNA with sequence homologous to miRNA-21. In order to further explore its practical application capabilities, the expression of miRNA in different cell lines was quantitatively analyzed and compared with the qRT-PCR. The considerable results of this study suggest great potential for the application of the proposed approach in clinical diagnosis.

Sustainable and cascaded catalytic hairpin assembly for amplified sensing of microRNA biomarkers in living cells

The sensing of intracellular microRNAs (miRNAs) is of significance for early-stage disease diagnosis and therapeutic monitoring. DNA is an interesting building material that can be programed into assemblies with rigid and branched structures, especially suitable for imaging intracellular biomolecules or therapeutic drug delivery. Here, by introducing the palindromic sequences into the programmable DNA hairpins, we describe an endogenous target-responsive three-way branched and palindrome-assisted catalytic hairpin assembly (3W-pCHA) approach for imaging miRNA-155 of living tumor cells with high sensitivity. The miRNA-155 triggers autonomous assembly of the fluorescently quenched signal hairpin and two hairpin dimers formed via hybridization of their respective palindromic sequences to yield branched DNA junctions, which carry the unopened hairpins and thus provide addressable substrates for continuous assembly formation of DNA nanostructures. During the formation of the DNA nanostructures, the miRNA-155 is cyclically reused and many signal probes are unfolded to show highly intensified fluorescence for detecting miRNA-155 down to 6.9 pM in vitro with high selectivity. More importantly, these probes can be transfected into live cancer cells to initiate the assembly process triggered by intracellular miRNA-155, which provides a new way for imaging highly under-expressed miRNAs in cells. Besides, this approach can also be employed to differentiate miRNA-155 expression variations in different cells, indicating its promising potentials for early-stage disease diagnosis and biological studies in cells.

Rational engineering the DNA tetrahedrons of dual wavelength ratiometric electrochemiluminescence biosensor for high efficient detection of SARS-CoV-2 RdRp gene by using entropy-driven and bipedal DNA walker amplification strategy

Fast and effective detection of epidemics is the key to preventing the spread of diseases. In this work, we constructed a dual-wavelength ratiometric electrochemiluminescence (ECL) biosensor based on entropy-driven and bipedal DNA walker cycle amplification strategies for detection of the RNA-dependent RNA polymerase (RdRp) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The entropy-driven cyclic amplification reaction was started by the SARS-CoV-2 RdRp gene to generate a bandage. The bandage could combine with two other single-stranded S1 and S2 to form a bipedal DNA walker to create the following cycle reaction. After the bipedal DNA walker completed the walking process, the hairpin structures at the top of the DNA tetrahedrons (TDNAs) were removed. Subsequently, the PEI-Ru@Ti₃C₂@AuNPs-S7 probes were used to combine with the excised hairpin part of TDNAs on the surface of Au-g-C₃N₄, and the signal change was realized employing electrochemiluminescence resonance energy transfer (ECL-RET). By combining entropy-driven and DNA walker cycle amplification strategy, the ratiometric ECL biosensor exhibited a limit of detection (LOD) as low as 7.8 aM for the SARS-CoV-2 RdRp gene. As a result, detecting the SARS-CoV-2 RdRp gene in human serum still possessed high recovery so that the dual-wavelength ratiometer biosensor could be used in early clinical diagnosis.

A Photoresponsive and Metal-Organic Framework Encapsulated DNA Tetrahedral Entropy-Driven Amplifier for High-Performance Imaging Intracellular MicroRNA

The further development of high-performance fluorescent biosensors to image intracellular microRNAs is beneficial to cancer medicine. By virtue of the need for enzymes and hairpin DNA probes, the entropy-driven reaction-assisted signal amplification strategy has shown an enormous potential to accomplish this task. Nevertheless, this good option still meets with poor biostability, low cell uptake efficiency, and unsatisfactory accuracy. On the basis of these challenges, we put forward here a battery of solving pathways. First, the straight DNA probes are anchored onto the vertexes of dual DNA tetrahedrons, and thus the enzyme resistance of the whole sensing system is observably enhanced. A metal-organic framework (ZIF-8 nanoparticle), which can be effectively dissociated into a weakly acidic environment, then is employed as an additional delivery vehicle to encapsulate such a DNA tetrahedron sustained biosensor and finally bring about a more efficient endocytosis. Last, a kind of photocleavage-linker triggered photoresponsive manner is incorporated to achieve an exceptional precise target identification, by which the biosensor can only be initiated under the irradiation of an externally mild 365 nm ultraviolet light source. In accordance with the above efforts, worthy assay performance toward microRNA-196a has given rise to this newly constructed biosensor, whose sensitivity is down to 2.7 pM and also able to distinguish single-base variation. Beyond that, the amplifier can work as a powerful imaging toolbox to accurately determine the targets in living cells, providing a promising intracellular sensing platform.

circ_0075943 Dominates the miR-141-3p/AK2 Network to Support the Development of Breast Carcinoma

Background

Breast cancer (BC) progression is related to the disorder of circular RNAs (circRNAs). This study aims to characterize the role of circ_0075943 in BC.

Methods

Real-time fluorescent quantitative PCR (real-time PCR) technology was implemented to investigate circ_0075943, AK2 mRNA, and microRNA-141-3p levels. MTT, colony formation method, Transwell, and flow cytometry technique were adopted to investigate cell function. The connection between miR-141-3p and circ_0075943 or AK2 was confirmed by the dual-luciferase reporter gene or RNA immunoprecipitation (RIP). The influence on circ_0075943 in vivo was confirmed by animal experiments.

Results

circ_0075943 was augmented in BC cell lines and tumor specimens. Dwindling of circ_0075943 could dramatically suppress the phenotype of BC cells and induce apoptosis. MiR-141-3p is a target of circ_0075943, and its repression largely reverses the influence of knocking down circ_0075943 on cell behavior. Moreover, AK2, as a target of miR-141-3p, is augmented in BC cells and specimens. AK2 overexpression could restore the phenotype of BC cells blocked by miR-141-3p redevelopment. Moreover, knocking down circ_0075943 could suppress the growth of tumors in vivo.

Conclusion

The abnormal regulation of circ_0075943 participates in part of the expansion of BC by dominating the miR-141-3p/AK2 regulatory network.

Amplifiable ratiometric fluorescence biosensing of nanosilver multiclusters populated in three-way-junction DNA branches

To explore the fluorescence bio-responsiveness of emissive silver nanoclusters (AgNCs) populated in DNA-branched scaffolds is intriguing yet challenging. In response to a desired targeting model (T*) as a vehicle, herein a customized three-way-junction DNA construct (TWJDC) is assembled via competitive hybridizing cascade among three stem-loop hairpins with specific base sequences, where the repeated recycling of T* enables the exponentially amplifiable output of rigid TWJDC. As designed, these stable hybridization products are highly T*-stimulated responsive and constructing-directional. In the three branched-arms, the unpaired sticky ends provide isotropic binding sites for a signaling hairpin encoded with two C-rich templates of green- and red-AgNCs clustering. The identical ligation of signal probe with three arms of TWJDC liberates its locked stem, enabling the separate growth of red-clusters in three branches. As demonstrated, three clusters of red-AgNCs possess advantageous self-enhancing fluorescent performance relative to single or two cluster(s), good biocompatibility and low cytotoxicity. Utilizing the bicolor AgNCs as dual-emitters with reversely changed emission intensity, we developed an innovative ratiometric strategy displaying sensitively linear dose-dependence on variable T* down to 1.9 pM, which can afford a promising platform for biosensing, bioanalysis, cell imaging, or even clinical theranostics.

Modular engineering of gold-silver nanocluster supermolecular structure endow strong electrochemiluminescence for ultrasensitive bioanalysis

Here, the gold-silver nanocluster supramolecular network (AuAg NCs) is synthesized by the assembly of Au nanoclusters (Au NCs) and Ag NCs via host-guest complexation between 6-aza-2-thiothymine as the stabilizer of Au NCs and L-arginine as the stabilizer of Ag NCs in solution, whose electrochemiluminescence (ECL) emission is not only exceptionally stronger than that of discrete monometallic NCs, but also more significant than that of agminated monometallic NCs. The dramatically enhanced ECL emission of self-assembled AuAg NCs originates from the synergistic effect of aggregation-induced enhancement and silver effect in gold catalysis. As a proof of concept, the self-assembled AuAg NCs is successfully applied in the ultrasensitive detection of breast cancer biomarker microRNAs-21 (miR-21), which guides a new pathway for creating high-quality nano-optical elements in chemical sensors, biological imaging, and lightemitting devices.

Exo III-Catalyzed Release of a Zn2+-Ligation DNAzyme to Drive the Strand Displacement Reaction and Gold Aggregation for the Homogeneous Bioassay of Kanamycin Antibiotics

Herein, we combine the exonuclease III (Exo III)-catalyzed release of a Zn²⁺-dependent ligation DNAzyme with the DNAzyme-driven strand displacement reaction (SDR) to develop a novel homogeneous colorimetric bioassay method for kanamycin (Kana) antibiotic detection. Upon the biorecognition reaction between Kana and a designed hairpin DNA, the DNAzyme-containing strand can be catalytically released by Exo III. Then, this DNAzyme will catalyze the ligation of two oligonucleotides to cause a SDR and the aggregation of gold nanoparticles (Au NPs) labeled by two linker DNA strands. Due to the aggregation of Au NPs for colorimetric signal transduction and the Exo III and SDR-assisted dual signal amplification, this method shows a wide linear range of 5 orders of magnitude and a very low detection limit down to 8.1 fg mL^-1. Together with its excellent selectivity, repeatability, reliability, and convenient manipulation, the proposed method shows a great potential for the food quality monitoring application.