A Both-End Blocked Peroxidase-Mimicking DNAzyme for Low-Background Chemiluminescent Sensing of miRNA

Impact of NH4+ on the catalytic activity of G-quadruplex/hemin DNAzyme for chemiluminescent sensing

G-quadruplex/hemin DNAzyme, a versatile tool for biosensing, is challenged by its low peroxidase-mimic activities. The addition of NH4+ may offer an efficient approach to improve its activity. However, the detailed impact of NH4+ on its catalytic activity remains unclear, confusing the selection of appropriate DNAzymes for biosensing applications. Here, we conducted a comprehensive examination of the influence of NH4+ on G-quadruplex/hemin DNAzyme. The results revealed that all DNAzymes with different G-quadruplex topologies exhibited increased catalytic activities in the presence of NH4+ relative to K+, followed by the subsequent activity order: parallel > hybrid > antiparallel. Further investigations indicated that the increased catalytic activity can be ascribed to the increased stability of the G-quadruplex/hemin complex, elevated reaction velocity, and improved substrate affinity. Leveraging the significant disparity in enzymatic activity between parallel and antiparallel G-quadruplexes, an allosteric sensor based on the Pb2+-induced topological conformation was developed for sensitive detection of Pb2+ in the NH4+-boosted G-quadruplex/hemin DNAzyme system (LOD, 1.56 nM), indicating potential for practical applications. Our discovery improves the understanding of NH4+-boosted G-quadruplex/hemin DNAzyme and may facilitate the development of biosensors.

Integration of RCA-Based DNA Nanoscaffold with Target Triggered RNA-Cleaving DNAzyme for Sensitive Detection of miRNA21

Cascaded amplification showed promising potential for detection of trace target miRNAs in molecular diagnosis and prevention of many diseases. In this study, miRNA21 was chosen as the target, and rolling circle amplification (RCA)-based DNA nanoscaffold was integrated with target triggered RNA-cleaving DNAzyme for sensitive detection of miRNA21. That is, the H1 probe was bound with the long-chain product of RCA to self-assemble into DNA nanoscaffold. Target miRNA21 triggered the hybridization chain reaction (HCR) located on the nanoscaffold, and led to rapid proximity of DNAzyme fragments modified at both ends of the H2 probe, which realized the cyclic cleavage of self-quenching substrate probe efficiently, and the fluorescence signal was restored. The results demonstrated that the proposed assay was sensitive, 0.76 pM of miRNA21 can be detected. The proposed assay was specific; only one-base mismatched miRNA21 can be effectively recognized, other nucleic acid sequence and the serum matrix did not cause any interference. The proposed assay was accurate; recoveries from 82.1 to 115.0% can be obtained in the spiked fetal bovine serum (FBS). The flexible and programmable characteristics of DNA nanoscaffold and DNAzyme provide a confident and robust strategy for more sensitive nucleic acid detection, and can be developed to be a universal sensing platform for detecting other miRNAs just needing modification on the corresponding sequence of H1 probe in HCR.

Integrating of analytical techniques with enzyme-mimicking nanomaterials for the fabrication of microfluidic systems for biomedical analysis

Bioanalysis faces challenges in achieving fast, reliable, and point-of-care (POC) determination methods for timely diagnosis and prognosis of diseases. POC devices often display lower sensitivity compared to laboratory-based methods, limiting their ability to quantify low concentrations of target analytes. To enhance sensitivity, the synthesis of new materials and improvement of the efficiency of the analytical strategies are necessary. Enzyme-mimicking materials have revolutionized the field of the fabrication of new high-throughput sensing devices. The integration of microfluidic chips with analytical techniques offers several benefits, such as easy miniaturization, need for low biological sample volume, etc., while also enhancing the sensitivity of the probe. The use enzyme-like nanomaterials in microfluidic systems can offer portable strategies for real-time and reliable detection of biological agents. Colorimetry and electrochemical methods are commonly utilized in the fabrication of nanozyme-based microfluidic systems. The review summarizes recent developments in enzyme-mimicking materials-integrated microfluidic analytical methods in biomedical analysis and discusses the current challenges, advantages, and potential future directions.

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.

A colorimetric and fluorescent dual-mode sensor based on bifunctional G-quadruplex-hemin complex for the determination of Pb2

Due to the threat of lead pollution to health, environmental and food safety, developing simple and fast detection methods is highly required. Whereas, traditional single-mode probe suffers from limited application scenario. In this study, a colorimetric and fluorometric dual-mode probe for Pb2+ determination was constructed by using bifunctional G-quadruplex-hemin complex. In this dual-mode probe, enzyme strand and substrate strand of 8-17 DNAzyme are labeled with G-quadruplex-hemin complex and fluorophore, respectively. In the absence of Pb2+, the self-assembly of enzyme strand and substrate strand inhibits intrinsic mimic peroxidase of G-quadruplex-hemin complex by base-pairing, which also quench the fluorescence via in proximity effect. When the DNAzyme is activated by Pb2+, the quenched fluorescence is restored as well as the inherent peroxidase mimetic activity, leading to dual signal output. Under optimal conditions, this dual-mode probe exhibit a good linear relationship between logarithm of Pb2+ concentration and signal difference within the range from 1.5 nM to 20 nM and 0.5 nM to 10 nM for colorimetric and fluorescence mode, respectively. The detection limits for the corresponding mode were estimated to be 1.29 nM and 0.16 nM, respectively. This dual-mode probe also successfully applied for the spiked river water assay with satisfactory recovery in the range of 93.2 %-115.3 %. This work paves a new way for DNAzyme based dual-mode probe construction.

Enhancing peroxidase-like activity of AuNPs through headspace reaction: A signal amplification strategy for colorimetric and fluorescent sensing of trace Hg2

BACKGROUND

Recently, headspace single-drop microextraction (HS-SDME) has attracted some attention for developing sensitive and selective colorimetric assays due to its excellent capability to reduce matrix interference and enrich analytes. However, the single droplet limits direct visual observation of color change and its quantitative measurement suffers from reduced optical path length. Therefore, amplifying the detection signals in both volume and intensity is an important and challenging task for improving the sensitivity, stability, and accuracy of such colorimetric analysis.

RESULTS

In this study, a "headspace-nanoenzyme" (HS-NE) strategy was proposed that successfully addressed these challenges and enabled the colorimetric and fluorescent dual-mode detection of trace Hg2+. Atomic Hg0, generated via chemical vapor generation (CVG), underwent headspace reaction with AuNPs droplet to form Au@HgNPs, thus catalyzing the oxidation of o-phenylenediamine (OPD) in the presence of H2O2. The absorbance and fluorescence intensity of oxidized OPD were proportion to the concentration of Hg2+ in the sample solution. Due to the greatly enhanced peroxidase-like activity by Au@HgNPs, the limit of detection was as low as 0.98 nM and 0.21 nM for the colorimetric and fluorescent modes, respectively. The applicability of this assay was further demonstrated with determination of Hg2+ in real environmental and biological samples. Moreover, a convenient and cost-effective paper-based sensing platform was fabricated for rapid on-site detection of Hg2+.

SIGNIFICANCE AND NOVELTY

This novel HS-NE strategy combines HS-SDME and nanoenzyme-based sensing to achieve dual effects of eliminating matrix interference and amplifying the measurement signal, resulting in improved accuracy, enhanced stability, high sensitivity, and exceptional selectivity, with great potential for on-site determination of trace Hg2+.

Colorimetric sensor array for discriminating and determinating phenolic pollutants basing on different ratio of ligands in Cu/MOFs

The high toxicity and low biodegradability of the phenolic pollutants destroyed the balance of the environment and influenced human health seriously. Here, we developed a three-dimensional coloremetric sensor array for discriminating and determinating phenolic pollutants basing on the distinct Cu/nucleotides MOFs. Firstly, three laccase-mimic Cu/MOFs (Cu/AMP, Cu/CMP, and Cu/GMP) were obtained by regulating the molar ratio of Cu2+ and nucleotides. Then the Cu/MOFs as the recognition elements of the sensor array catalyzed the pollutants-4-AAP-H2O2 system, obtaining the colored benzoquinone products. Subsequently, the data array obtaining from the combined training matrix (3 Cu/MOFs × 6 pollutants × 5 replicates) was projected into a new dimensional space to obtain the 3D canonical scores, and classified into individual clusters by introducing LDA method. No overlap in their respective LDA plots for the six phenolic pollutants with different concentrations suggested the prominent discriminating performance of the sensor array. Furthermore, the sensor array exhibited high selectivity compared to the "lock-and-key" sensors even other active matrices coexisting in water samples. Importantly, the most influential discrimination factor was used to monitor the levels of the six targets, evidencing the potential application in assessing water pollution and maintaining human health.

Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors

miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.

Self-Powered DNAzyme Walker Enables Dual-Mode Biosensor Construction for Electrochemiluminescence and Electrochemical Detection of MicroRNA

Herein, an electrochemiluminescence (ECL) and electrochemical (EC) dual-mode biosensor platform with a self-powered DNAzyme walking machine was established for accurate and sensitive detection of miRNA-21. By employing a magnesium ion (Mn²⁺)-dependent DNAzyme cleavage cycling reaction, the walking machine was built by assembling DNAzyme walking strands and ferrocene (Fc)-labeled substrate strands on the Au nanoparticles and graphitic carbon nitride nanosheet (g-C₃N₄ NS)-covered electrode. The DNAzyme walking strand was first prohibited by a blocker strand. After the addition of target miRNA-21 and Mn²⁺, the DNAzyme walker could be activated and produce autonomous movements along the electrode track fueled by Mn²⁺-dependent DNAzyme-catalyzed substrate cleavage without additional energy supply. Notably, each walking step resulted in the cleavage of a substrate strand and the release of a Fc-labeled DNA strand fragment, allowing us to acquire an extreme ECL signal recovery of g-C₃N₄ inhibited by Fc. Meanwhile, numerous Fc-labeled DNA fragments escaped from the surface of the electrode, directly producing an obvious decrease in the square wave voltammetry (SWV) signal from Fc on the same sensing platform. This work not only avoided difficultly assembling various signal indicators but also significantly improved the sensitivity through using self-powered DNAzyme-walker amplification. Moreover, the proposed design employed the same reaction to produce two signal output modes, which could eliminate the interference from diverse reactive pathways on the outcome to mutually improve the accuracy. Therefore, the dual-mode miRNA-21 biosensor exhibited wide detection ranges of 100 aM to 100 nM with low detection limits of 54.3 and 78.6 aM by ECL and SWV modes, respectively, which provided an efficient and universal biosensing approach with extensive applications in early disease diagnosis and bioanalysis.

An overview of biochemical technologies for the cancer biomarker miR-21 detection

In recent years, the incidence of cancer has continuously increased, in which various miRNAs have been proposed as biomarkers for the early screening of cancer patients. As a consequence, the development of accurate methods for miRNA quantification has become a major research challenge worldwide. As one of the first discovered oncogenic miRNAs, microRNA-21 (miR-21) has been highlighted for its critical role in cancers. This review describes the main techniques currently available for miR-21 detection, compares the differences of the methods and the amplification strategies, and provides an overview of the state of knowledge in the field.

Visual Assay for Methicillin-Resistant Staphylococcus aureus Based on Rolling Circular Amplification Triggering G-Quadruplex/Hemin DNAzyme Proximity Assembly

Nowadays, infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have constituted a new challenge for anti-infective treatment. Precise identification and rapid clinical diagnostics of MRSA from other methicillin-sensitive strains entail assays with robust diagnostic efficiency and simple operation steps. Sensitive detection of MecA gene is promising to indicate MRSA infection, but it is challenged by the lack of isothermal and simple strategies. A visual assay based on isothermal rolling circular amplification and G-quadruplex/hemin (G4/hemin) DNAzyme proximity assembly was proposed for the immediate, efficient, and cost-effective detection of MecA in simple operation steps and in a single tube. The presence of MecA specifically drove the formation of circular templates, which further triggered isothermal amplification. The amplified product offered abundant binding sites for DNA-grafted hemin probes to form a novel proximity-assembled G4/hemin DNAzyme structure for colorimetric changing diagnosis. This tandem-repeated novel DNAzyme possessed higher catalytic activity and a lower background signal than traditional G4/hemin DNAzyme, ensuring sensitive discrimination of MRSA (limit of detection: 9.6 pM). Assay stability and antimatrix interference capability enable clinical application, which shows compared diagnostic ability with classic methods (100% sensitivity and 100% specificity) but possesses more simplified procedures and shorter turnaround time (<6 h). This colorimetric strategy in a nonsite-specific and hypersensitive manner holds foreseeable prospects in clinical diagnostic and research applications.

Visual/Photoelectrochemical Off-On Sensor Based on Cu/Mn Double-Doped CeO2 and Branched Sheet Embedded Cu2O/CuO Nanocubes

An integrated dual-signal bioassay was devised to fulfil thrombin (TB) ultrasensitive detection by integrating visualization with the photoelectrochemical technique based on G-quadruplex/hemin. During the process, branched sheet embedded copper-based oxides prepared with illumination and alkaline condition play a vital role in obtaining the desirable photocurrent. The switchover of photoelectrochemical signal was realized by the adjustable distance between electron acceptor G-quadruplex/hemin and interface materials due to dissociation of the Cu/Mn double-doped cerium dioxide (CuMn@CeO₂)/DNA caused by the addition of TB. Then, CuMn@CeO₂ transferred onto visual zones triggered catalytic reactions under the existence of 3,3',5,5'-tetramethylbenzidine and hydrogen peroxide, making a variation in color recognized by the naked eye and providing visual prediction. Under optimized conditions, this bioassay protocol demonstrated wide linear ranges (0.0001-50 nM), high selectivity, stability, and reproducibility. More importantly, the proposed visual/photoelectrochemical transduction mechanism platform exhibits a lower background signal and more reliable detection results, which also offers an effective way for detecting other proteins and nucleic acids.

Aggregation-Induced Emission Effect within Peroxyoxalate-Loaded Mesoporous Silica Nanoparticles for Efficient Harvest of Chemiluminescence Energy in Aqueous Solutions

Aggregation-induced emission (AIE) molecules that can avoid the aggregation-caused quenching (ACQ) effect and break the concentration limit have been widely used for biosensing. Similar to fluorescence dyes, AIE molecules can be chemiexcited simply by a peroxyoxalate-based chemiluminescence (CL) reaction, but the hydrolysis of peroxyoxalate is often a problem in an aqueous solution. Herein, we report an AIE effect within peroxyoxalate-loaded silica nanoparticles (PMSNs) for an efficient harvest of CL energy as well as alleviation of bis(2,4,5-trichloro-6-carbopentoxyphenyl) oxalate (CPPO) hydrolysis. Peroxyoxalate (i.e., CPPO) and AIE molecules (i.e., 1,2-benzothiazol-2-triphenylamino acrylonitrile, BTPA) were loaded together within the mesoporous silica nanoparticles (MSNs) to synthesize the BTPA-PMSN nanocomposite. The BTPA-PMSNs not only allowed CPPO to be dispersed well in an aqueous solution but also avoided the hydrolysis of CPPO. Meanwhile, the proximity between BTPA and CPPO molecules in the mesopores of MSNs facilitated the BTPA aggregate to harvest the energy from CL intermediates. Hence, the CL system of BTPA-PMSNs can work efficiently in aqueous solutions at a physiological pH. The CL quantum yield of the BTPA-PMSN system was measured to be 9.91 × 10^-5, about 20 000-fold higher than that obtained in the rhodamine B (RhB, a typical ACQ dye)-PMSN system. Using BTPA-PMSNs for H₂O₂ sensing, a limit of detection (LOD) as low as 5 nM can be achieved, 1000-fold lower than that achieved in the RhB-PMSNs system. Due to the feasibility of working at a physiological pH, this CL system is also quite suitable for the detection of oxidase substrates such as glucose and cholesterol. This BTPA-PMSN CL system with the merits of high CL quantum yield at a physiological pH is appealing for biosensing.

Development of DNA Biosensors Based on DNAzymes and Nucleases

DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.

Recent progress of SERS optical nanosensors for miRNA analysis

This review focuses on emerging applications of surface-enhanced Raman spectroscopy (SERS) optical nanosensors for miRNA analysis, in which the key enhancement factors of the SERS signal, i.e. SERS-active substrates, SERS nanoprobes and nano-assembly strategy, are emphasized. This article includes many nanomaterials for miRNA analysis by the SERS technique. We summarize these reported nanomaterials mainly according to their function in the miRNA assay biosensor. We also briefly summarize the research progress of these nanomaterials in SERS detection of intracellular miRNA. Finally, we discussed the prospect and limitations of SERS nanosensors for analyzing miRNA.

An ultrasensitive biosensor for dual-specific DNA based on deposition of polyaniline on a self-assembled multi-functional DNA hexahedral-nanostructure

Kras and Braf are major oncogenes. The mutation of Kras codon 12 or Braf V600E can lead to ovarian carcinoma. The detection of oncogene-related DNAs and their mutations offers solution for early diagnosis of ovarian cancer. Herein, a size-tunable multi-functional DNA hexahedral-nanostructure (DHN) has been rationally designed and modified on the electrode to response to Kras and Braf DNA. The size of DHN is controlled via polyadenines (polyA). The complete self-assembly of DHN depends on the presence of both target DNAs and two assistant probes. Meanwhile, a HRP-mimicking DNAzyme forms in DHN, which catalyzes the polymerization of aniline. The produced polyaniline is utilized as the output signal through differential pulse voltammetry (DPV). The biosensor shows the linear range from 100 fM to 1 μM, with the detection limit of 48.7 fM for Kras gene; and the linear range from 100 fM to 100 nM, with the detection limit of 44.1 fM for Braf gene, respectively. Since the current response depends on both gene sequences, the high specificity of the biosensor endows it to operate in an "OR"-type logic gate to discriminate the mutation of both genes. When Kras codon 12 or Braf V600E mutation happens, the response decreases significantly due to the incomplete formation of DNAzyme in DHN. The practicability of the biosensor has been verified through challenging human serum samples. Thus, it has great potential for clinical diagnosis of ovarian cancer through simultaneous detection of Kras and Braf genes and their mutations.

Ultrasensitive Nucleic Acid Assay Based on Cyclometalated Iridium(III) Complex with High Electrochemiluminescence Efficiency

This work developed a sensitive electrochemiluminescence (ECL) biosensor based on a cyclometalated iridium(III) complex ((bt)₂Irbza), which was synthesized for the first time. Annihilation, reductive-oxidative, and oxidative-reductive ECL behaviors of (bt)₂Irbza were investigated, respectively. The oxidative-reductive ECL intensity was the strongest compared with the other two, which showed 16.7 times relative ECL efficiency compared with commercial [Ru(bpy)₃]²⁺ under the same experimental conditions. Therefore, an ECL biosensing system with (bt)₂Irbza as the anodic luminophore was established for miRNA detection based on a closed bipolar electrode (BPE). Combined with both steric hindrance and catalytic effects induced by hemin/G-quadruplex in the cathodic reservoir of BPE that changed the Faraday current of the cathode and thus mediated the ECL intensity of (bt)₂Irbza in the anode of BPE, the ECL sensor stated an ultrahigh sensitivity for microRNA (miRNA-122) analysis with a detection limit of 82 aM.

Suppressing the background activity of hemin for boosting the sensitivity of DNAzyme-based biosensors by SYBR Green I

Peroxidase-like DNAzymes have been extensively used to replace horseradish peroxidase (HRP) for developing biosensors for signal amplification. However, the background activity from the cofactor (i.e., free hemin) has limited the sensitivity of such sensors. Herein, we aim to find an inhibitor for hemin to suppress the background signal, and a classic split DNAzyme-based sensor was used to detect a complementary DNA oligonucleotide. After screening a series of dyes, SYBR Green I (SG, one of the DNA stanning dyes) was selected for suppressing the background. Simply by adding 0.84 μM SG, the background from 50 nM hemin was suppressed over 30-fold. The suppression was caused by the interaction between SG and hemin. In the presence of the target DNA, the formed duplex region and G-quadruplex structure can better bind SG and hemin respectively, thus preventing the interaction between them and showing a high activity of the DNAzyme. The optimized sensor showed a detection limit of 3.8 pM for the target DNA (p53 gene). In addition, the backgrounds from chemiluminescence, colorimetric and fluorescence sensing modes can all be reduced by adding SG to the split DNAzyme system. The suppression of the background of peroxidase DNAzymes is a critical step towards practical use of related biosensors.

A Novel Cell-Assisted Enhanced Chemiluminescence Strategy for Rapid and Label-Free Detection of Tumor Cells in Whole Blood

In this study, an interesting phenomenon was found where cells (including tumor and normal cells) managed to significantly enhance chemiluminescence (CL) signals. The possible reaction mechanism may be that cells can be severely damaged by CL substrates, and the released contents, possibly proteins (such as cytochrome c), can remarkably magnify CL owing to the increased production of singlet oxygen. More importantly, based on the above phenomena, a novel cell-assisted enhanced CL strategy was proposed for the rapid and label-free detection of tumor cells. The complexes of aptamer sgc8c and streptavidin-modified magnetic beads were employed to recognize and isolate target tumor cells from whole blood. The enhanced CL intensity, which was triggered directly by the captured cells, was measured. The proposed strategy exhibited a good detection performance with a linear range from 200 to 10,000 cells/mL. The analysis can be finished in ∼30 min, and the limit of detection was down to 100 cells/mL. The recoveries and relative standard deviations were 97.81-102.71% and 3.46-12.71%, respectively. Moreover, the established method can successfully distinguish the leukemia patients from healthy people. Therefore, it provides a novel, rapid, and simple method for the determination of tumor cells, which can be used in further practice.

Hemin-Bridged MOF Interface with Double Amplification of G-Quadruplex Payload and DNAzyme Catalysis: Ultrasensitive Lasting Chemiluminescence MicroRNA Imaging

Here, we report a double-amplified sensing platform for ultrasensitive chemiluminescence (CL) miRNA detection in real patients' blood in which a hemin-bridged metal-organic framework (MOF) is employed as a functional interface to boost the payload and catalysis of G-quadruplex (G4) DNAzymes. Hemin is here used as the organic ligand for the MOF synthesis, which endows the MOF with an intrinsic peroxidase-like catalytic activity. Most importantly, the MOF surface provides a large amount of binding sites for polymeric G4 DNAzymes that are produced by miRNA-triggered rolling circle amplification reactions, and meanwhile, the interfaced G4 DNAzymes on MOFs (G4/MOFzymes) display an about 100-fold higher catalytic activity than those in solution. By using the G4/MOFzyme catalysts in the luminol/H₂O₂ CL system, the amplification detection of two acute myocardial infarction (AMI)-related miRNAs (low to 1 fM seen with naked eyes) is achieved in human serum with a smartphone as a portable imaging detector, which provides a facile methodology for point-of-care (POC) diagnosis of AMI. Compared with previous smartphone-based counterparts not requiring sophisticated equipment, this new facile methodology shows both 6 orders of magnitude higher sensitivity and an ∼50-fold longer duration for CL miRNA imaging. These unique features allow our developed G4/MOFzymes to be further employed as a novel luminescent ink for printing commonly used patterns.

Biosensors for epigenetic biomarkers detection: A review

Epigenetic inheritance is a heritable change in gene function independent of alterations in nucleotide sequence. It regulates the normal cellular activities of the organisms by affecting gene expression and transcription, and its abnormal expression may lead to the developmental disorder, senile dementia, and carcinogenesis progression. Thus, epigenetic inheritance is recognized as an important biomarker, and the accurate quantification of epigenetic inheritance is crucial to clinical diagnosis, drug development and cancer treatment. Noncoding RNA, DNA methylation and histone modification are the most common epigenetic biomarkers. The conventional biosensors (e.g., northern blotting, radiometric, mass spectrometry and immunosorbent biosensors) for epigenetic biomarkers assay usually suffer from hazardous radiation, complicated manipulation, and time-consuming procedures. To facilitate the practical applications, some new biosensors including colorimetric, luminescent, Raman scattering spectroscopy, electrochemical and fluorescent biosensors have been developed for the detection of epigenetic biomarkers with simplicity, rapidity, high throughput and high sensitivity. In this review, we summarize the recent advances in epigenetic biomarkers assay. We classify the biosensors into the direct amplification-free and the nucleotide amplification-assisted ones, and describe the principles of various biosensors, and further compare their performance for epigenetic biomarkers detection. Moreover, we discuss the emerging trends and challenges in the future development of epigenetic biomarkers biosensors.

A DNAzyme-amplified DNA circuit for highly accurate microRNA detection and intracellular imaging

A rationally and modularly engineered CHA-HCR-DNAzyme circuit was constructed for amplified biosensing and bioimaging with high performance.

Biomolecular self-assembly circuits have been well developed for high-performance biosensing and bioengineering applications. Here we designed an isothermal concatenated nucleic acid amplification system which is composed of a lead-in catalyzed hairpin assembly (CHA), intermediate hybridization chain reaction (HCR) and ultimate DNAzyme amplifier units. The analyte initiates the self-assembly of hairpin reactants into dsDNA products in CHA, which generates numerous trigger sequences for activating the subsequent HCR-assembled long tandem DNAzyme nanowires. The as-acquired DNAzyme catalyzed the successive cleavage of its substrates, leading to an amplified fluorescence readout. The sophisticated design of our CHA-HCR-DNAzyme scheme was systematically investigated in vitro and showed dramatically enhanced detection performance. As a general sensing strategy, this CHA-HCR-DNAzyme method enables the amplified analysis of miRNA and its accurate intracellular imaging in living cells, originating from their synergistic signal amplifications. This method shows great potential for analyzing trace amounts of biomarkers in various clinical research studies.

Ultrasensitive photoelectrochemical biosensor for MiRNA-21 assay based on target-catalyzed hairpin assembly coupled with distance-controllable multiple signal amplification

Here, with the target-catalyzed hairpin assembly generated dsDNA (HP1-HP2) to synchronously control the departure of quencher ferrocene and approach of sensitizer methylene blue, a distance-controllable multiple signal amplification based photoelectrochemical biosensor was proposed for MiRNA-21 assay.

A versatile dynamic light scattering strategy for the sensitive detection of microRNAs based on plasmonic core-satellites nanoassembly coupled with strand displacement reaction

A low-cost, effective and enzyme-free sensing strategy for ultrasensitive microRNA (miRNA) detection was developed based on dynamic light scattering (DLS) coupled with strand displacement reaction (SDR). The combination of DLS and SDR was used to assess the size changes of core-satellites nanoassembly. This strategy realized the limit of detection (LOD) as low as 0.24 pM (S/N = 3) and the detection range of 5 pM-150 pM, which might urge this strategy as an ideal candidate for the sensitive detection of miRNA in the future. In addition, the proposed strategy could be successfully used to analyze target miRNA in various cancer cells, indicating that the developed SDR-DLS strategy has promising clinical implications for rapid and early diagnosis of cancer-related diseases.

Amplified MicroRNA Detection and Intracellular Imaging Based on an Autonomous and Catalytic Assembly of DNAzyme

Abnormal microRNAs (miRNAs) expression is demonstrated to associate with various important biological processes, including tumorigenesis, metastasis, and progression. Given the low miRNA expression at the earlier stage of diseases, its amplified detection still requires more efforts. Inspired by the two-stage arithmetic amplifier of electric devices, we reported an autonomous and catalytic assembly of DNAzyme strategy by integrating a DNAzyme biocatalyst and catalytic hairpin assembly (CHA) circuit. Here the catalytically inactive DNAzyme subunits were respectively grafted into these metastable CHA hairpin reactants that were kinetically impeded without false cross-hybridizations. The target catalyzed the nonenzymatic CHA-mediated successive assembly of dumbbell-like bis-DNAzyme nanostructures, leading to the efficient DNAzyme-mediated cleavage of fluorophore/quencher-modified substrate and to the generation of an amplified fluorescence signal. The present CHA-DNAzyme amplifier can be employed as a versatile and general sensing platform for analyzing other analytes (e.g., miRNA) by introducing a sensing module into the present system. Moreover, the homogeneous CHA-DNAzyme method could realize the sensitive intracellular miRNA imaging in living cells, which is attributed to the inherently synergistic amplification property between DNAzyme and CHA reactions. Given the attractive analytical features of the autonomous CHA-DNAzyme system, the present strategy shows great promise for analyzing additional different analytes in clinical research fields.

A G-triplex based molecular beacon for label-free fluorescence "turn-on" detection of bleomycin

Since bleomycins (BLMs) play a prominent role in the clinical treatment of various cancers, the development of convenient and sensitive detection assays for BLM is of great significance in cancer therapy and related biological mechanism research. Here, taking advantage of the easily controllable and excitation of the G-triplex DNA structure, we reported a facile, label-free G-triplex based functional molecular beacon (G3MB) sensing system for fluorescence "turn-on" detection of BLM based on BLM-Fe(ii) mediated DNA strand scission. In the presence of BLM, the stable hairpin structure of G3MB undergoes an irreversible cleavage in the loop region that contains a 5'-GT-3' recognition site for BLM. The released G-tract DNA fragment self-assembles into a G-triplex-ThT complex showing a strong fluorescence. Owing to the effective locking of G-tracts in the stem of the G3MB and the specific DNA strand scission by BLM which is like a key for the release of G-tracts, the assay shows high sensitivity and selectivity with a detection limit of 0.2 nM. In addition, satisfactory results were obtained for the detection of BLM in human serum samples. Critically, the convenient "mix-and-detect" protocol, fast response and no need for modifying DNA offered a potential application of the proposed strategy for BLM assay in biomedical and clinical studies.

Universal and label-free photosensitization colorimetric assays enabled by target-induced termini transformation of dsDNA resistant to Exo III digestion

A label-free and universal colorimetric assay was developed via the combination of CHA, Exo III digestion, and photosensitization colorimetry.

Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications

DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.

Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA structure

A novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA) was established by combining Y-shaped DNA duplex and G-quadruplex-hemin DNAzyme. A G-rich single-stranded DNA (Oligo-1) displays peroxidase mimicking catalytic activity due to the specific binding with hemin in the presence of K+, which was able to catalyze the oxidation of colorless 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS2-) by H2O2 to generate green ABTS•- radical for colorimetric assay. Oligonucleotide 2 (Oligo-2) was partly complementary with Oligo-1 and the target DNA. Upon addition of target DNA, Oligo-1, Oligo-2 and target DNA can hybridize with each other to form Y-shaped DNA duplex. The DNAzyme sequence of Oligo-1 was partly caged into Y-shaped DNA duplex, resulting in the inactivation of the DNAzyme and a sharp decrease of the absorbance of the oxidation product of ABTS2-. Under the optimum condition, the absorbance decreased linearly with the concentration of target DNA over the range of 1.0-250 nM and the detection limit was 0.95 nM (3σ/slope) Moreover, satisfied result was obtained for the discrimination of single-base or two-base mismatched DNA.

Improving the Signal-to-Background Ratio during Catalytic Hairpin Assembly through Both-End-Blocked DNAzyme

Catalyzed hairpin assembly (CHA) is an important DNA engineering tool for a variety of applications such as DNA nanotechnology and biosensing. Here we report a hairpin-type of both-end-blocked DNAzyme to improve the signal-to-background ratio during the CHA process. In the design, the DNAzyme activity can be blocked efficiently via locking both ends of the G-rich DNAzyme sequence in the loop and stem (blocking efficiency = 96%) and can be easily recovered during the CHA process (activation efficiency = 94%). The both-end-blocked DNAzyme is by far the most sensitive optical detection mode for monitoring the CHA process that can be used for determination of 0.05 fmol miRNA-21. The fabricated CHA-DNAzyme sensing system was also able to discriminate miRNA-21 from single-/three-base mismatch miRNA-21. The feasibility of real application was also tested via detection of miRNA-21 levels in tumor cell samples. Therefore, the sensing system with the advantages of convenience, high sensitivity, and selectivity is an appealing strategy for miRNA detection.

Electro-Grafted Electrode with Graphene-Oxide-Like DNA Affinity for Ratiometric Homogeneous Electrochemical Biosensing of MicroRNA

This work demonstrated for the first time a simple and rapid approach to endow the electrode with the excellent discrimination ability over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) through the robust electrochemical grafting of in situ generated 1-naphthalenesulfonate (NS^-) diazonium salt onto the surface of indium tin oxide (ITO) electrode. On the basis of understanding the influence of sequence and length on the binding affinity of ssDNA and dsDNA toward NS^- grafted ITO (NS^--ITO) electrode, these interesting findings were successfully employed to rationally develop a ratiometric homogeneous electrochemical biosensing platform for microRNA based on the affinity-mediated signal transduction. The achievement of ultrasensitive detection of microRNA lies in a compatibly designed T7 exonuclease-assisted isothermal amplification strategy, in which the presence of target microRNA initiated the continual and opposite affinity inversion of two rationally engineered electrochemical signal reporters, methylene blue (MB) labeled hairpin reporter and ferrocene (Fc) labeled dsDNA reporter, toward NS^--ITO electrode, thereby providing the ratiometric transduction and amplification of the homogeneous electrochemical output signal. By measuring the distinct variation in the peak current intensity ratios of Fc and MB tags, this ratiometric homogeneous electrochemical microRNA biosensing platform showed a detection limit of 25 aM, which is much lower than that of the reported homogeneous electrochemical biosensors. Therefore, we envision that the proposed approach will find useful applications in disease molecular diagnoses and biomedicine.