Amplified detection of DNA through the enzyme-free autonomous assembly of hemin/G-quadruplex DNAzyme nanowires

Highly sensitive miRNA-21 detection with enzyme-free cascade amplification biosensor

In this study, we present an enzyme-free fluorescence biosensor for the highly sensitive detection of miRNA-21, a crucial biomarker in clinical diagnosis. Our innovative approach combines catalytic hairpin assembly (CHA) and entropy-driven amplification into a cascade amplification strategy. MicroRNA initiates the catalytic hairpin assembly reaction, liberating the trigger region needed for the entropy-driven amplification reaction. This triggers a series of strand displacement reactions, resulting in the separation of the fluorescence resonance energy transfer pair and an amplified fluorescence signal from FAM. Our cascade amplification strategy achieves ultra-sensitive microRNA detection, with an impressive limit of detection (LOD) of 1.3 fM, approximately 100-fold lower than CHA alone. Additionally, we successfully applied this biosensor for microRNA quantification in human serum and cell lysates, demonstrating its practicality and potential for early diagnosis.

Improved Catalytic Activity of Spherical Nucleic Acid Enzymes by Hybridization Chain Reaction and Its Application for Sensitive Analysis of Aflatoxin B1

Conventional spherical nucleic acid enzymes (SNAzymes), made with gold nanoparticle (AuNPs) cores and DNA shells, are widely applied in bioanalysis owing to their excellent physicochemical properties. Albeit important, the crowded catalytic units (such as G-quadruplex, G4) on the limited AuNPs surface inevitably influence their catalytic activities. Herin, a hybridization chain reaction (HCR) is employed as a means to expand the quantity and spaces of G4 enzymes for their catalytic ability enhancement. Through systematic investigations, we found that when an incomplete G4 sequence was linked at the sticky ends of the hairpins with split modes (3:1 and 2:2), this would significantly decrease the HCR hybridization capability due to increased steric hindrance. In contrast, the HCR hybridization capability was remarkably enhanced after the complete G4 sequence was directly modified at the non-sticky end of the hairpins, ascribed to the steric hindrance avoided. Accordingly, the improved SNAzymes using HCR were applied for the determination of AFB1 in food samples as a proof-of-concept, which exhibited outstanding performance (detection limit, 0.08 ng/mL). Importantly, our strategy provided a new insight for the catalytic activity improvement in SNAzymes using G4 as a signaling molecule.

Imaging mRNA in vitro and in vivo with nanofirecracker probes via intramolecular hybridization chain reaction

Hybridization chain reaction (HCR) based enzyme-free amplification techniques have recently been developed for the visualization of intracellular messenger RNA (mRNA). However, the slow kinetics and potential interference with the intricate biological environments hinder its application in the clinic and in vivo. Herein, we designed a nanofirecracker probe-based strategy using intramolecular hybridization chain reaction (IHCR) amplifier for rapid, efficient, sensitive, specific detection and imaging of survivin mRNA both in vitro and vivo. Two probes, HP1 and HP2, in IHCR were simultaneously incorporated into a DNA nanowire scaffolds to bring HP1 and HP2 to close proximity on the assembled nanowire scaffolds. Empowered by the DNA nanowire scaffolds and spatial confinement effect, the nanofirecracker probe-based IHCR sensing system exhibited improved biostability, accelerated reaction kinetics, and enhanced signal amplification. This new strategy has been successfully applied to imaging mRNA in both cultured cells and in mice. Importantly, this novel sensing method was capable of detecting survivin mRNA in clinical blood samples from subjects with colorectal cancer. Thus, this novel nanofirecracker probe-based IHCR strategy holds great potential in advancing both biomedical research and in molecular diagnostics.

DNA-Functionalized Porphyrinic Metal-Organic Framework-Based Drug Delivery System for Targeted Bimodal Cancer Therapy

A DNA-functionalized porphyrinic MOF (porMOF) drug delivery system was successfully constructed. porMOF as a photosensitizer and drug delivery carrier can integrate photodynamic therapy (PDT) and chemotherapy. Via the strong coordination interaction between the zirconium cluster of porMOF and the terminal phosphate group of DNA, the stable modification of the DNA layer on the porMOF surface is achieved. Meanwhile, the introduction of C/G-rich base pairs into the DNA double-stranded structure provides more binding sites of chemotherapeutic drug doxorubicin (DOX). AS1411, an aptamer of nucleolin proteins that are overexpressed by cancer cells, is introduced in the double-stranded terminal, which can endow the nanosystem with the ability to selectively recognize cancer cells. C-rich sequences in DNA double strands form an i-motif structure under acidic conditions to promote the highly efficient release of DOX in cancer cells. In vitro and in vivo experiments demonstrate that the synergistic PDT/chemotherapy modality achieves highly efficient cancer cell killing and tumor ablation without undesirable side effects.

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.

Accelerated Hybridization Chain Reaction Kinetics Using Poly DNA Tetrahedrons and Its Application in Detection of Aflatoxin B1

Traditional hybridization chain reaction (HCR) as a popular isothermal amplification technique shows some inevitable disadvantages in bioanalysis due to its relatively slow kinetics, which could be markedly promoted when the HCR initiator occurs under tension. Herein, a poly DNA tetrahedrons (pTDNs)-mediated HCR was successfully constructed to make its initiator in a stretched state by long-range electrostatic forces owing to the superimposed electrostatic interactions derived from the synthesized pTDNs, and it was hypothesized that it could remarkably enhance HCR performance, which was testified by theoretical simulations and experimental studies. Consequently, pTDNs-mediated HCR was applied to develop a novel immunoassay for rapid and sensitive detection of aflatoxin B1 as a proof-of-concept, and its signal amplification was attributed to the increased G4 DNAzyme that loaded on the second antibody. Our work paves a promising way using simple DNA frameworks alone to heighten HCR kinetics for reaction speed improvement and signal amplification in bioanalysis.

Ratiometric Detection of Zn2+ Using DNAzyme-Based Bioluminescence Resonance Energy Transfer Sensors

While fluorescent sensors have been developed for monitoring metal ions in health and diseases, they are limited by the requirement of an excitation light source that can lead to photobleaching and a high autofluorescence background. To address these issues, bioluminescence resonance energy transfer (BRET)-based protein or small molecule sensors have been developed; however, most of them are not highly selective nor generalizable to different metal ions. Taking advantage of the high selectivity and generalizability of DNAzymes, we report herein DNAzyme-based ratiometric sensors for Zn2+ based on BRET. The 8-17 DNAzyme was labeled with luciferase and Cy3. The proximity between luciferase and Cy3 permiQed BRET when coelenterazine, the substrate for luciferase, was introduced. Adding samples containing Zn2+ resulted in a cleavage of the substrate strand, causing dehybridization of the DNAzyme construct, thus increasing the distance between Cy3 and luciferase and changing the BRET signals. Using these sensors, we detected Zn2+ in serum samples and achieved Zn2+ detection with a smartphone camera. Moreover, since the BRET pair is not the component that determines the selectivity of the sensors, this sensing platform has the potential to be adapted for the detection of other metal ions with other metal-dependent DNAzymes.

RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy

Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.

Transient Transcription Machineries Modulate Dynamic Functions of G-Quadruplexes: Temporal Regulation of Biocatalytic Circuits, Gene Replication and Transcription

Native G-quadruplex-regulated temporal biocatalytic circuits, gene polymerization, and transcription processes are emulated by biomimetic, synthetically engineered transcription machineries coupled to reconfigurable G-quadruplex nanostructures. These are addressed by the following example: (i) A reaction module demonstrates the fuel-triggered transcription machinery-guided transient synthesis of G-quadruplex nanostructures. (ii) A dynamically triggered and modulated transcription machinery that guides the temporal separation and reassembly of the anti-thrombin G-quadruplex aptamer/thrombin complex is introduced, and the transient thrombin-catalyzed coagulation of fibrinogen is demonstrated. (iii) A dynamically fueled transient transcription machinery for the temporal activation of G-quadruplex-topologically blocked gene polymerization circuits is introduced. (iv) Transcription circuits revealing G-quadruplex-promoted or G-quadruplex-inhibited cascaded transcription machineries are presented. Beyond advancing the rapidly developing field of dynamically modulated G-quadruplex DNA nanostructures, the systems introduce potential therapeutic applications.

Heme-Dependent Supramolecular Nanocatalysts: A Review

Enzymes fold into three-dimensional structures to distribute amino acid residues for catalysis, which inspired the supramolecular approach to construct enzyme-mimicking catalysts. A key concern in the development of supramolecular strategies is the ability to confine and orient functional groups to form enzyme-like active sites in artificial materials. This review introduces the design principles and construction of supramolecular nanomaterials exhibiting catalytic functions of heme-dependent enzymes, a large class of metalloproteins, which rely on a heme cofactor and spatially configured residues to catalyze diverse reactions via a complex multistep mechanism. We focus on the structure-activity relationship of the supramolecular catalysts and their applications in materials synthesis/degradation, biosensing, and therapeutics. The heme-free catalysts that catalyze reactions achieved by hemeproteins are also briefly discussed. Towards the end of the review, we discuss the outlook on the challenges related to catalyst design and future prospective, including the development of structure-resolving techniques and design concepts, with the aim of creating enzyme-mimicking materials that possess catalytic power rivaling that of natural enzymes..

Fluorescence Enhancement Method for Aptamer-Templated Silver Nanoclusters and Its Application in the Construction of a β-Amyloid Oligomer Sensor

DNA-templated silver nanoclusters (DNA-AgNCs) have attracted significant attention due to their unique fluorescence properties. However, so far, the relatively low quantum yields of the DNA-AgNCs and the complex design of DNA-AgNC-based sensors have limited their application in biosensing or bioimaging. Herein, we report a novel fluorescence enhancement method. The β-Amyloid Oligomer (AβO) aptamer (Apt_AβO) with A₁₀/T₁₀ at its 3' end can be directly used as the template to fabricate the AgNCs. When the AgNCs were hybridized with the complementary strand that has 12 bases suspended at its 3' terminal, being the same or complementary to the A/T at the 3' end of the Apt_AβO, and two-base mismatches in the complementary region of the aptamer excluded A₁₀/T₁₀, a dramatic fluorescence enhancement (maximum: ∼500-fold; maximum quantum yield: 31.5%) can be realized. The fluorescence enhancement should result from the aggregation-induced emission of the AgNCs, which can be attributed to forming the reticular structure of the hybridized product. To some extent, the method developed in this work is extendable. The fluorescence enhancement was also realized from the thrombin aptamer-templated AgNCs through designing the aptamer and the corresponding complementary strand according to the method. Based on the fluorescence enhancement of the Apt_AβO-templated AgNCs, an "on-off" fluorescence sensor was constructed for the sensitive and selective detection of AβO. This work provides a rational strategy to realize fluorescence enhancement for the aptamer-templated AgNCs and design an aptamer-based fluorescence sensor.

Accurate detection of reactive oxygen species by tuning an elastic motif (GPGGA)4 in nanopores

We have developed a reactive oxygen species (ROS) sensor based on nanopores modified with GGGCEG(GPGGA)₄CEG. The formation of an intramolecular disulfide bond oxidized by ROS leads to conformation changes in GGGCEG(GPGGA)₄CEG, which then induces an obvious change in the size of the nanopores and a corresponding ionic current change. This work allows the accurate and dynamic monitoring of ROS through the combination of (GPGGA)₄ and nanopores.

MXene supported biomimetic bilayer lipid membrane biosensor for zeptomole detection of BRCA1 gene

A biomimetic bilayer lipid membrane supported MXene based biosensor is reported for electrochemical hybridization detection of the most prevalent and potential BC biomarker BRCA1. 2D MXene nanosheet-anchored gold nanoparticle-decorated biomimetic bilayer lipid membrane (AuNP@BLM) biosensor is used for the attachment of thiolated single-stranded DNA (HS-ssDNA) targeting hybridization detection. The interaction of biomimetic bilayer lipid membrane with 2D MXene nanosheets is explored in this work for the first time. The synergistic combination of MXene and AuNP@BLM has proven to efficiently improve the detection signal to several folds. The sensor provides hybridization signals only to the complementary DNA (cDNA) sequence with a linearity range 10 zM to 1 µM and LOD of 1 zM without the need of any further amplification. The specificity of the biosensor is validated using non-complementary (ncDNA) and double base mis-match oligonucleotide DNA (dmmDNA) sequences. The sensor successfully distinguishes the signal for different target DNAs with good reproducibility indicated by the RSD value of 4.9%. Hence, we envision that the reported biosensor can be used to construct efficient diagnostic point-of-care tools based on molecular affinity interactions.

Catalyst-Accelerated Circular Cascaded DNA Circuits: Simpler Design, Faster Speed, Higher Gain

DNA cascaded circuits have great potential in detecting low abundance molecules in complex biological environment due to their powerful signal amplification capability and nonenzymatic feature. However, the problem of the cascaded circuits is that the design is relatively complex and the kinetics is slow. Herein, a new design paradigm called catalyst-accelerated circular cascaded circuits is proposed, where the catalyst inlet is implanted and the reaction speed can be adjusted by the catalyst concentration. This new design is very simple and only requires three hairpin probes. Meanwhile, the results of a series of studies demonstrate that the reaction speed can be accelerated and the sensitivity can be also improved. Moreover, endogenous mRNA can also be used as a catalyst to drive the circuits to amplify the detection of target miRNA in live cells and in mice. These catalyst-accelerated circular cascaded circuits can substantially expand the toolbox for intracellular low abundance molecular detection.

A novel highly sensitive compilation-detachment fluorescence sensing strategy based on RNA-cleavage DNAzyme for MDA-MB-231 breast cancer biomarker determination

Herein, we designed a novel and highly sensitive fluorescence multicomponent detachable platform for MDA-MB-231 breast cancer cell detection as a model. The RNA cleavage DNAzyme was used as a central operator of the multicomponent probe through which compilation and induced detachment of probe was done. During the compilation step, the dsDNA-Sybr green 1 complexes on gold nanoparticles (GNP@dsDNA@SG1) were assembled. The intercalated Sybr green in the DNA structure has been used as an amplified signal generator on one site of DNAzyme and magnetic nanoparticles (MNP) act as a biological carrier and probe collector on the opposite side. The enzyme activator co-factor (MDA-MB-231 cell cytoplasmic protein) provokes the activation of the catalytic core of enzyme sequence in the DNAzyme molecule, followed by cleavage reaction in the substrate sequence and releasing GNP@ dsDNA@SG1 into the solution. The results indicate that the Sybr green emission fluorescence (520 nm) increases with the increment of MDA-MB-231 protein concentration in the linear dynamic range of 8.10 × 10^-2 to 1.95 ng ml^-1 (0.77 × 10^-3-0.019 cell ml^-1) with a detection limit (LOD) of 1/72 × 10^-2 pg ml^-1 under optimal conditions. The proposed immunosensor has great potential in developing ultrasensitive and rapid diagnostic platforms.

Detection of Hepatitis C virus RNA using a novel hybridization chain reaction method that competitively dampens cascade amplification

The hybridization chain reaction (HCR) is widely used for biosensing. However, HCR does not provide the required sensitivity. In this study, we reported a method to improve the sensitivity of HCR by dampening the cascade amplification. First, we designed a biosensor based on HCR, and an initiator DNA was used to trigger the cascade amplification. Optimization of the reaction was then performed, and the results showed that the limit of detection (LOD) for the initiator DNA was about 2.5 nM. Second, we designed a series of inhibitory DNAs to dampen the HCR cascade amplification, and DNA dampeners (50 nM) were applied in the presence of the DNA initiator (50 nM). One of the DNA dampeners (D5) showed the best inhibitory efficiency of greater than 80%. This was further applied at concentrations ranging from 0 nM to 10 nM to prohibit the HCR amplification caused by a 2.5 nM initiator DNA (the limit of detection for this initiator DNA). The results showed that 0.156 nM of D5 could significantly inhibit the signal amplification (p<0.05). Additionally, the limit of detection for the dampener D5 was 16 times lower than that for the initiator DNA. Based on this detection method, we achieved a detection limit as low as 0.625 nM for HCV-RNAs. In summary, we developed a novel method with improved sensitivity to detect the target designed to prohibit the HCR cascade. Overall, this method could be used to qualitatively detect the presence of single-stranded DNA/RNA.

The recent advancements in the early detection of cancer biomarkers by DNAzyme-assisted aptasensors

Clinical diagnostics rely heavily on the detection and quantification of cancer biomarkers. The rapid detection of cancer-specific biomarkers is of great importance in the early diagnosis of cancers and plays a crucial role in the subsequent treatments. There are several different detection techniques available today for detecting cancer biomarkers. Because of target-related conformational alterations, high stability, and target variety, aptamers have received considerable interest as a biosensing system component. To date, several sensitivity-enhancement strategies have been used with a broad spectrum of nanomaterials and nanoparticles (NPs) to improve the limit and sensitivity of analyte detection in the construction of innovative aptasensors. The present article aims to outline the research developments on the potential of DNAzymes-based aptasensors for cancer biomarker detection.

Development and validation of a label-free colorimetric aptasensor based on the HCR and hemin/G-quadruplex DNAzyme for the determination of patulin in fruits and fruit-based products from Xinjiang (China)

In this study, a simple, novel and practical label-free colorimetric aptasensor was successfully prepared for the ultrasensitive detection of patulin, based on the hybridization chain reaction (HCR) and hemin/G-quadruplex DNAzyme-signal amplification strategy. In this aptasensor, a detection probe was designed consisting of the aptamer sequence for the patulin and an initiator sequence to trigger the HCR. Two hairpin structures (H1 and H2) that included the G-quadruplex sequences in inactive configuration were used as functional elements. The presence of patulin triggered the opening of the hairpin structure and the beginning of the HCR. After the addition of hemin, G-rich DNA self-assembled into the peroxidase-mimicking hemin/G-quadruplex DNAzymes, which catalyzed a colorimetric reaction. Under optimized conditions, patulin was measured within a linear range of 0.1-200 ng mL^-1, and the detection limit was 0.060 ng mL^-1. The recovery rates ranged from 91.4 to 105% for fruits and fruit-based products. Subsequently, a total of 311 samples comprising fruits, fruit-based products and dried fruits were collected from supermarkets, production bases and farmers' markets in Xinjiang, and analyzed for patulin using the proposed aptasensor. Patulin was detected in 16 samples (5.14%) at concentrations ranging from 1.23 to 16.4 μg kg^-1. None of the samples exceeded the maximal level set by the EU commission (50 μg kg^-1). The positivity in fresh fruits (7.69%) was significantly higher than that of fruit-based products (4.00%) and dried fruits (1.25%). In summary, the proposed aptasensor can quickly detect patulin in food samples, thus providing a warning for mycotoxin contamination.

Development of a Novel Tissue Blot Hybridization Chain Reaction for the Identification of Plant Viruses

Assays for the high throughput screening of crops for virus monitoring need to be quick, easy, and low cost. One method involves using tissue blot immunoassays (TBIA), where plant stems are blotted onto nitrocellulose membrane and screened with available antibodies against a range of viruses. TBIAs are inexpensive but limited by antibody availability and specificity. To circumvent the antibody limitations, we developed the tissue blot hybridization chain reaction (TB-HCR). As with TBIA, plant stems are blotted onto a nitrocellulose membrane, however, TB-HCR involves using nucleic acid probes instead of antibodies. We demonstrated for the first time that TB-HCR can be used for plant viruses by designing and testing probes against species from several virus genera including begomovirus, polerovirus, luteovirus, cucumovirus, and alfamovirus. We also explored different hairpin reporter methods such as biotin/streptavidin-AP and the Alexa Fluor-488 Fluorophore. TB-HCR has applications for low-cost diagnostics for large sample numbers, rapid diagnostic deployment for new viruses, and can be performed as a preliminary triage assay prior to downstream applications.

Cationic Copolymer-Augmented DNA Hybridization Chain Reaction

Various DNA assembly techniques and structures have emerged with the continuous progress of DNA nanotechnology. DNA hybridization chain reaction (HCR) is a representative example owing to isothermal and enzyme-free features. However, HCR is time consuming and is inhibited by nucleases present in biological samples. Herein, we demonstrated that a cationic copolymer, poly(l-lysine)-graft-dextran (PLL-g-Dex), significantly facilitated HCR and increased its initiator sensitivity by 40-fold. PLL-g-Dex promoted the generation of HCR products with high molecular weight by accelerating the initiation and the subsequent growth steps of HCR. Moreover, PLL-g-Dex protected the HCR system from nucleases, permitting HCR in the presence of serum components. Addition of PLL-g-Dex is a universal and efficient strategy that does not require optimization of the reactor setup or DNA sequences, thus laying a solid foundation for the wider application of HCR.

Switchable and dynamic G-quadruplexes and their applications

G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO₂ nanoparticles or metal-organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.

Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures

Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.

Regulating Spatial Localization and Reactivity Biasness of DNAzymes by Metal Ions and Oligonucleotides

Chemical gradient sensing behavior of catalytically active colloids and enzymes is an area of immense interest owing to their importance in understanding fundamental spatiotemporal complexity pattern in living systems and designing of dynamic materials. Herein, we have shown peroxidase activity of DNAzyme (G-quadruplex-hemin complex tagged in a micron-sized glass bead) can be modulated by metal ions and metal ion-binding oligonucleotides. Next we demonstrated both experimentally and theoretically that the localization and product formation ability of the DNAzyme containing particle remains biased to the more catalytically active zone where concentration of metal ion (Hg2+) inhibitor is low. Interestingly, this biased localization can be broken by introduction of Hg2+ binding oligonucleotide in the system. Additionally, macroscopically asymmetric catalytic product distributed zone has also been achieved on this process, showing possibility in regulation in autonomous spatially controlled chemical process. This demonstration of autonomous modulation of the localization pattern and spatially specific enhanced product forming ability of DNAzymes will further enable in designing of responsive nucleic acid-based motile materials and surfaces.

Unified-amplifier based primer exchange reaction (UniAmPER) enabled detection of SARS-CoV-2 from clinical samples

Primer exchange reaction (PER) is an emergent method for non-templated synthesis of single stranded DNA molecules. PER has been shown to be effective in cell imaging systems and for detection of macromolecules. A particular application of PER is to detect a specific target nucleic acid. To this endeavor, two coupled DNA hairpins, a detector and an amplifier, play in accordance to extend a target nucleic acid with a concatemer DNA sequence. Here we introduced unified-amplifier based primer exchange reaction (UniAmPER) that beneficially extends the target by a unified-amplifier. The unified-amplifier operates as both detector and amplifier hairpins. The extension resulted in synthesis of concatemer G-rich sequences. The G-rich sequences were expected to form G-quadruplex (GQ) structures. Presence of the GQ structures were investigated by peroxidase activity of GQs in presence ^{of hemin, H}2°2 ^{and 3,3',5,5'-Tetramethylbenzidine (TMB) as well as by fluorescence signal} generation upon intercalation of thioflavin T (ThT). The presented unified-amplifier in this study facilitates application of PER systems for development of colorimetric or fluorogenic biosensors. As a proof of principle, the method has been applied for detection of reversely transcribed cDNAs from clinical SARS-CoV-2 samples.

Versatile Photoelectrochemical Biosensing for Hg2+ and Aflatoxin B1 Based on Enhanced Photocurrent of AgInS2 Quantum Dot-DNA Nanowires Sensitizing NPC-ZnO Nanopolyhedra

Eliminating false positives or negatives in analysis has been a challenge. Herein, a phenomenon of polarity-switching photocurrent of AgInS₂ quantum dot (QD)-DNA nanowires reversing nitrogen-doped porous carbon-ZnO (NPC-ZnO) nanopolyhedra was found for the first time, and a versatile photoelectrochemical (PEC) biosensor with a reversed signal was innovatively proposed for dual-target detection. NPC-ZnO is a photoactive material with excellent PEC properties, while AgInS₂ QDs as a photosensitive material match NPC-ZnO in the energy level, which not only promotes the transfer of photogenerated carriers but also switches the direction of PEC current. Furthermore, in order to prevent spontaneous agglomeration of AgInS₂ (AIS) QDs and improve its utilization rate, a new multiple-branched DNA nanowire was specially designed to assemble AgInS₂ QDs for constructing amplified signal probes, which not only greatly increased the load of AgInS₂ QDs but also further enhanced the photoelectric signal. When the target Hg²⁺-induced cyclic amplification process generated abundant RDNA, the DNA nanowire signal probe with plenty of QDs was linked to the NPC-ZnO/electrode by RDNA, generating greatly amplified polarity-reversed photocurrent for signal "ON" detection of Hg²⁺. After specific binding of the target (aflatoxin B1, AFB1) to its aptamer, the signal probes of AIS QD-DNA nanowires were released, realizing signal "OFF" assay of AFB1. Thus, the proposed new PEC biosensor provides a versatile method for detection of dual targets and also effectively avoids both false positive and negative phenomena in the assay process, which has great practical application potential in both environmental and food analysis.

Target biorecognition-triggered assembly of a G-quadruplex DNAzyme-decorated nanotree for the convenient and ultrasensitive detection of antibiotic residues

The abuse of kanamycin (Kana) in many fields has led to increasing antibiotic pollution problems and serious threats to public health. Therefore, determining how to develop methods to realize the convenient detection of antibiotics in complicated environmental matrices is highly desirable. In this study, we utilized a target biorecognition-triggered hybridization chain reaction (HCR) assembly of a G-quadruplex DNAzyme (G-DNAzyme)-decorated nanotree to develop a novel homogeneous colorimetric biosensing method for the convenient and ultrasensitive detection of Kana antibiotic residues in real samples. Through the designed aptamer-recognition reaction, an Mg²⁺-dependent DNAzyme (MNAzyme) strand can be liberated. Thus, its catalyzed cleavage of the hairpin substrates anchored at a DNA nanowire will cause the assembled formation of an HCR-initiator; this process can be greatly amplified by the exonuclease III-assisted target recycling and the MNAzyme-catalyzed release of another MNAzyme strand. Based on the DNA-nanowire-accelerated HCR assembly of many G-DNAzyme-decorated DNA duplexes on the two sides of the nanowire, a DNA nanotree decorated by numerous G-DNAzymes will form to realize the ultrasensitive colorimetric signal output. Under the optimal conditions, this method exhibited a wide five-order-of-magnitude linear range and a very low detection limit of 28 fg mL^-1. In addition, excellent selectivity, repeatability, and reliability were also demonstrated for this homogeneous bioassay method. These unique features along with its automatic manipulation and low assay cost show promise for practical applications.

miRNA-Guided Imaging and Photodynamic Therapy Treatment of Cancer Cells Using Zn(II)-Protoporphyrin IX-Loaded Metal-Organic Framework Nanoparticles

An analytical platform for the selective miRNA-21-guided imaging of breast cancer cells and miRNA-221-guided imaging of ovarian cancer cells and the selective photodynamic therapy (PDT) of these cancer cells is introduced. The method is based on Zn(II)-protoporphyrin IX, Zn(II)-PPIX-loaded UiO-66 metal-organic framework nanoparticles, NMOFs, gated by two hairpins H_i/H_j through ligation of their phosphate residues to the vacant Zr⁴⁺-ions associated with the NMOFs. The hairpins are engineered to include the miRNA recognition sequence in the stem domain of H_i, and in the H_i and H_j, partial locked stem regions of G-quadruplex subunits. Intracellular phosphate-ions displace the hairpins, resulting in the release of the Zn(II)-PPIX and intracellular miRNAs open H_i, and this triggers the autonomous cross-opening of H_i and H_j. This activates the interhairpin hybridization chain reaction and leads to the assembly of highly fluorescent Zn(II)-PPIX-loaded G-quadruplex chains. The miRNA-guided fluorescent chains allow selective imaging of cancer cells. Moreover, PDT with visible light selectively kills cancer cells and tumor cells through the formation of toxic reactive oxygen species.

Zippered G-quadruplex/hemin DNAzyme: exceptional catalyst for universal bioanalytical applications

G-quadruplex (G4)/hemin DNAzyme is promising horseradish peroxidase (HRP)-mimic candidate in the biological field. However, its relatively unsatisfactory catalytic capacity limits the potential applications. Inspired by nature protease, we conducted a proximity-enhanced cofactor assembly strategy (PECA) to form an exceptional HRP mimic, namely zippered G4/hemin DNAzyme (Z-G4/H). The hybridization of short oligonucleotides induced proximity assembly of the DNA-grafted hemin (DGH) with the complementary G4 sequences (cG4s), mimicking the tight configuration of protease cofactor and apoenzyme. The detailed investigations of catalytic efficiency and mechanism verified the higher activity, more rapid catalytic rate and high environmental tolerance of the Z-G4/H than the classical G4/hemin DNAzymes (C-G4/H). Furthermore, a proximity recognition transducer has been developed based on the PECA for sensitive detection of gene rearrangement and imaging human epidermal growth factor receptor 2 protein (HER2) dimerization on cell surfaces. Our studies demonstrate the high efficiency of Z-G4/H and its universal application potential in clinical diagnostics and biomolecule interaction research. It also may offer significant opportunities and inspiration for the engineering of the protease-free mimic enzyme.

A new G-triplex-based strategy for sensitivity enhancement of the detection of endonuclease activity and inhibition

EcoRI is an important biomacromolecule in live cells and protects bacterial cells against foreign DNA. In this work, we developed a simple and convenient G-triplex (G3) (5′-TGGGAAGGGAGGGAATTCCCT-3′)-based colorimetric assay for the rapid and selective detection of EcoRI activity and inhibition. The sequence specifically responds to EcoRI in the presence of K⁺ and hemin to form a G-triplex/hemin complex. Taking advantage of G-triplex, EcoRI activity was investigated under the optimized conditions. The absorption intensity ratio displayed a linear relationship against the concentration of EcoRI in the range 0 to 100 U mL⁻¹, and the detection limit was 5.7 U mL⁻¹. Furthermore, G3 showed good selectivity, and the ability to be used to screen for EcoRI inhibitors, indicating its potential in detection and analysis applications.

A new G-triplex-based probe was developed for detecting EcoRI activity and inhibition. The probe showed good selectivity towards EcoRI. The assay was colorimetric and can be monitored by the naked eye.

Living-Cell MicroRNA Imaging with Self-Assembling Fragments of Fluorescent Protein-Mimic RNA Aptamer

As the cellular roles of RNA abundance continue to increase, there is an urgent need for the corresponding tools to elucidate native RNA functions and dynamics, especially those of short, low-abundance RNAs in live cells. Fluorescent RNA aptamers provide a useful strategy to create the RNA tag and biosensor devices. Corn, which binds with 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO), is a good candidate for the RNA tag because of its enhanced photostability and red-shifted spectrum. Herein, we report for the first time the utilization of Corn as a split aptamer system, combined with RNA-initiated fluorescence complementation (RIFC), for monitoring RNA self-assembly and sensing microRNA. In this platform, the 28-nt Corn was divided into two nonfunctional halves (named probe I and probe II), and an additional target RNA recognition and stem part was introduced in each probe. The target RNA can trigger the self-assembly reconstitution of the Corn's G-quadruplex scaffold for DFHO binding and turn-on fluorescence. These probes can be transfected stably into mammalian cells and deliver the light-up fluorescent response to microRNA-21 (miR-21). Significantly, the probes have good photostability, with minimal fluorescence loss after continuous irradiation, and can be used for imaging of miR-21 in living mammalian cells. The proposed method is universal and could be applied to the sensing of other tumor-associated RNAs, including messenger RNA and noncoding RNA, as well as for monitoring RNA/RNA interactions. The Corn-based splitting aptamers show promising potential in the real-time visualization and mechanistic analysis of nucleic acids.

Hybridization chain reaction and its applications in biosensing

To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.

Portable microfluidic device with thermometer-like display for real-time visual quantitation of Cadmium(II) contamination in drinking water

Cadmium (Cd²⁺) is a toxic metal ion widely existing in water, soil and food. Conventional water quality control heavily relies on expensive, bulky and sophisticated instrument such as spectrometry, which is time-consuming and incompatible with on-site, real-time detection. Here, a portable microfluidic device with thermometer-like visual readouts is developed for real-time quantitation of cadmium (II) contamination in drinking water. We use Cd²⁺-dependent DNAzyme (Cd16), which is cleaved when Cd²⁺ is present, creating a single strand DNA which triggers catalytic hairpin assembly (CHA) with two hairpins H1 and H2 as the building blocks. Plenty of H1H2 complex, the product after the Cd²⁺-mediated CHA, are generated, which can connect magnetic microparticles (MMPs) and polystyrene microparticles (PMPs), forming "MMPs-H1H2-PMPs" sandwich structure. To provide visual readout to quantitate the particle connection, the particle solution is loaded into a portable microfluidic chip. A magnetic separator first removes MMPs and the connected PMPs, while free PMPs can continue flowing until accumulating into a bar at the particle dam. Shown as a thermometer-like display, the accumulating length is inversely proportional to the concentration of Cd²⁺, enabling quantitative detection of Cd²⁺ by the naked eye. The proposed device exhibits a limit of detection of 11.3 nM of Cd²⁺, selectivity >200-fold against other metal ions, high tolerance to the interferents present in drinking water and high recovery rate in tap water. With high analytical performance without any sample preparation step, this portable device is highly promising in real-time monitoring in urban drinking water at sites.

A label-free fluorescent aptasensor based on HCR and G-quadruplex DNAzymes for the detection of prostate-specific antigen

Prostate specific antigen (PSA) has been considered as the most potential serological biomarker for the early stage detection of prostate cancer. Here, a label-free fluorescence aptasensing strategy for detecting PSA based on hybridization chain reaction (HCR) and G-quadruplex DNAzymes has been developed. This designed strategy consists of three DNA probes, aptamer probe (AP), hairpin probe 1 (H1) and hairpin probe 2 (H2). In the presence of target PSA, the aptamer sequences in AP specifically recognized PSA to form a PSA-aptamer complex, causing an AP conformation change and thus releasing the initiator, which triggered the chain-like assembly of H1 and H2 that yielded extended nicked double-stranded DNA through HCR. Upon the addition of hemin, the G-rich segments at the end of H1 and H2 self-assembled into the peroxidase-mimicking hemin/G-quadruplex DNAzymes, which catalyzed the hydrogen peroxide-mediated oxidation of thiamine to give a fluorescence signal dependent on the concentration of PSA. Under optimal conditions, a limit of detection of 0.05 nM and a linear range from 0.1 nM to 1 nM (R2 = 0.9942) were achieved by this assay. In addition, other interfering proteins, such as IgG, AFP and CEA, did not produce any significant change in the fluorescence intensity response, indicating good selectivity of this sensor for PSA detection. Finally, this proposed aptasensor was successfully used for diluted serum samples.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

Single-Molecule FRET-Based Dynamic DNA Sensor

Selective and sensitive detection of nucleic acid biomarkers is of great significance in early-stage diagnosis and targeted therapy. Therefore, the development of diagnostic methods capable of detecting diseases at the molecular level in biological fluids is vital to the emerging revolution in the early diagnosis of diseases. However, the vast majority of the currently available ultrasensitive detection strategies involve either target/signal amplification or involve complex designs. Here, using a p53 tumor suppressor gene whose mutation has been implicated in more than 50% of human cancers, we show a background-free ultrasensitive detection of this gene on a simple platform. The sensor exhibits a relatively static mid-FRET state in the absence of a target that can be attributed to the time-averaged fluorescence intensity of fast transitions among multiple states, but it undergoes continuous dynamic switching between a low- and a high-FRET state in the presence of a target, allowing a high-confidence detection. In addition to its simple design, the sensor has a detection limit down to low femtomolar (fM) concentration without the need for target amplification. We also show that this sensor is highly effective in discriminating against single-nucleotide polymorphisms (SNPs). Given the generic hybridization-based detection platform, the sensing strategy developed here can be used to detect a wide range of nucleic acid sequences enabling early diagnosis of diseases and screening genetic disorders.

Zr4+-mediated hybrid chain reaction and its application for highly sensitive electrochemical detection of protein kinase A

An electrochemical platform has been developed to detect protein kinase activity through the combined actions of Zr⁴⁺ mediated signal transition and hybridization chain reaction (HCR)-stimulated DNAzymes nanowires. First of all, protein kinase A (PKA) phosphorylates substrate peptides immobilized on gold electrode surface. Thereafter, the DNA1 containing 5'-phosphoryl ends is linked to the phosphorylated substrate peptide via the robust phosphate-Zr⁴⁺-phosphate linkages. By the introduction of molecular beacons (MBs), the DNA1 can open the hairpin structures of MBs through toehold mediated strand displacement (TMSDR), leading to an autonomous stem-opening process and subsequent assembly of G-quadruplex-containing DNA chains by HCR. After the addition of hemin, the formed HRP-mimicking DNAzymes can catalyze the hydroquinone-H₂O₂ system to generate amplified electrochemical signals. As expected, this method can achieve ultrahigh analytical performance with a low detection limit of 0.02U/mL and exhibit high cost-savings potential without the need for antibody, protease and labeling. Therefore, this method can serve as a new tool for the assay of protein kinase A and its inhibitor screening in the future.

Stochastic Collision Electrochemistry from Single G-Quadruplex/Hemin: Electrochemical Amplification and MicroRNA Sensing

Stochastic collision electrochemistry is a hot topic in single molecule/particle research, which provides an opportunity to investigate the details of the single molecule/particle reaction mechanism that is always masked in ensemble-averaged measurements. In this work, we develop an electrochemical amplification strategy to monitor the electrocatalytic behavior of single G-quadruplex/hemin (GQH) for the reaction between hydrogen peroxide and hydroquinone (HQ) through the collision upon a gold nanoelectrode. The intrinsic peroxidase activities of single GQH were investigated by stochastic collision electrochemical measurements, giving further insights into understanding biocatalytic processes. Based on the unique catalytic activity of GQH, we have also designed a hybridization chain reaction strategy to detect miRNA-15 with good selectivity and sensitivity. This work provided a meaningful strategy to investigate the electrochemical amplification and the broad application for nucleic acid sensing at the single molecule/particle level.

Multiplexed and amplified chemiluminescence resonance energy transfer (CRET) detection of genes and microRNAs using dye-loaded hemin/G-quadruplex-modified UiO-66 metal-organic framework nanoparticles

Dye-loaded UiO-66 metal-organic framework nanoparticles (NMOFs) modified with catalytic hemin/G-quadruplex DNAzyme labels act as functional hybrid modules for the chemiluminescence resonance energy transfer (CRET) analysis of miRNAs (miRNA-155 or miRNA-21) or genes (p53 or BRCA1). The dye-loaded NMOFs (dye = fluorescein (Fl) or rhodamine 6G (Rh 6G)) are modified with hairpin probes that are engineered to include in their loop domains recognition sequences for the miRNAs or genes, and in their stem regions caged G-quadruplex domains. In the presence of the analytes miRNAs or genes, the hairpin structures are opened, leading, in the presence of hemin, to the self-assembly of hemin/G-quadruplex DNAzyme labels linked to the dye-loaded NMOFs. In the presence of luminol and H2O2, the hemin/G-quadruplex DNAzyme labels catalyze the generation of chemiluminescence that provides radiative energy to stimulate the process of CRET to the dye loaded in the NMOFs, resulting in the luminescence of the loaded dye without external excitation. The resulting CRET signals relate to the concentrations of the miRNAs or the genes and allow the sensitive analysis of miRNAs and genes. In addition, the DNA hairpin-functionalized dye-loaded NMOF sensing modules were further applied to develop amplified miRNA or gene CRET-based sensing platforms. The dye-loaded NMOFs were modified with hairpin probes that include in their loop domain the recognition sequences for miRNA-155 or miRNA-21 or the recognition sequences for the p53 or BRCA1 genes. Subjecting the hairpin-modified NMOFs to the respective miRNAs or genes, in the presence of two hairpins H i and H j that include in their stem regions caged G-quadruplex subunit domains, results in the analyte-triggered opening of the probe hairpin linked to the NMOFs, and the opened hairpin tethers induce the cross-opening of the hairpins H i and H j by the hybridization chain reaction, HCR, resulting in the assembly of G-quadruplex wires tethered to the NMOFs. The binding of hemin to the HCR-generated chains yields hemin/G-quadruplex DNAzyme wires that enhance, in the presence of luminol/H2O2, the CRET processes in the hybrid nanostructures. These amplification platforms lead to the amplified sensing of miRNAs and genes. By mixing the Fl- and Rh 6G-loaded hairpin-functionalized UiO NMOFs, the multiplexed CRET detection of miRNA-155, miRNA-21 and the p53 and BRCA1 genes is demonstrated.

The Recent Development of Hybridization Chain Reaction Strategies in Biosensors

With the continuous development of biosensors, researchers have focused increasing attention on various signal amplification strategies to pursue superior performance for more applications. In comparison with other signal amplification strategies, hybridization chain reaction (HCR) as a powerful signal amplification technique shows its certain charm owing to nonenzymatic and isothermal features. Recently, on the basis of conventional HCR, this technique has been developed and improved rapidly, and a variety of HCR-based biosensors with excellent performance have been reported. Herein, we present a systematic and critical review on the research progress of HCR in biosensors in the last five years, including the newly developed HCR strategies such as multibranched HCR, migration HCR, localized HCR, in situ HCR, netlike HCR, and so on, as well as the combination strategies of HCR with isothermal signal amplification techniques, nanomaterials, and functional DNA molecules. By illustrating some representative works, we also summarize the advantage and challenge of HCR in biosensors, and offer a deep discussion of the latest progress and future development trends of HCR in biosensors.

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.