Biosensing with DNAzymes

Biosensor-based methods for exosome detection with applications to disease diagnosis

Exosomes are nanoscale extracellular vesicles (EVs) secreted by most eukaryotic cells and can be found in nearly all human body fluids. Increasing evidence has revealed their pivotal roles in intercellular communication, and their active participation in myriad physiological and pathological activities. Exosomes' functions rely on their contents that are closely correlated with the biological characteristics of parental cells, which may provide a rich resource of molecular information for accurate and detailed diagnosis of a diverse array of diseases, such as differential diagnosis of Alzheimer's disease, early detection and subtyping of various tumors. As a category of sensitive detection devices, biosensors can fully reveal the molecular information and convert them into actionable clinical information. In this review, recent advances in biosensor-based methods for the detection of exosomes are summarized. We have described the fabrication of various biosensors based on the analysis of exosomal proteins, RNAs or glycans for accurate diagnosis, with respect to their elaborate recognition designs, signal amplification strategies, sensing properties, as well as their application potential. The challenges along with corresponding technologies in the future development and clinical translation of these biosensors are also discussed.

Cascade-amplification-based electrochemical detection of Akashiwo sanguinea at pre-outbreak stage

Red tide events caused by Akashiwo sanguinea (A. sanguinea) pose a significant threat to ecosystems. However, studies that offer promising approaches for portable and onsite detection with precise identification of A. sanguinea remain insufficient. In this study, we developed an electrochemical biosensor (E-biosensor) for detecting A. sanguinea combined with cascade amplification strategies, termed TDW-E-biosensor. A predictive relationship was also established to predict algal cell density based on electrochemical signals. The experiment results showed that the TDW-E-biosensor was successfully applied for detecting A. sanguinea at the pre-outbreak stage and demonstrated excellent analytical performance, showing a low limit of detection (LOD) of 0.0676 fM and quantitation (LOQ) of 0.102 fM for the three-electrode system, and a low LOD of 6.873 fg μL-1 and LOQ of 20.460 fg μL-1 for the portable system. The accuracy of the TDW-E-biosensor was validated through comparison with droplet digital PCR (ddPCR) and Bland-Altman analysis, demonstrating a high level of agreement (a mean difference of 0.132 and a standard deviation of 0.184). The reliability of the predictive relationship was evidenced by controlled laboratory experiments and Bland-Altman analysis. The developed TDW-E-biosensor provides an innovative and promising tool for early warning efforts regarding harmful algae.

Functional nucleic acid-based fluorescence imaging for tumor microenvironment monitoring: A review

BACKGROUND

The tumor microenvironment (TME) refers to the complex ecological system surrounding tumor cells, which is intimately associated with regulating tumor cell growth, invasive behavior, and metastatic capacity. Hence, in situ imaging of related bioactivity with resolution in the TME is critical for early cancer detection and accurate diagnosis. In recent years, fluorescence imaging technology has become a widely used tool in TME research due to its non-invasive nature, high spatiotemporal resolution, and capability for real-time monitoring. Among these advancements, signal probes designed based on functional nucleic acids (FNAs) provide a promising and innovative toolkit for targeted imaging analysis of the TME.

RESULTS

This review provides a comprehensive discussion on the construction of FNA-based biosensors and their advancements in TME monitoring. In this review, we initially provide a systematic summary of the current targeting strategies of FNA-based biosensors for visual monitoring of the TME, focusing on targeting cell surface and extracellular matrix components. Subsequently, we further explore the application of FNA-based biosensors in monitoring the TME. These biosensors have successfully achieved the monitoring of key parameters, bioactive molecules and other tumor markers in the tumor microenvironment due to their excellent molecular recognition ability and high sensitivity. Finally, we discuss some of the challenges currently faced in the field. In response to these challenges, we propose potential research directions and look forward to the future development prospects of this field.

SIGNIFICANCE

Unlike previous reviews of biosensors based on FNAs for imaging tumor markers in the TME, this work is the first to review how such biosensors can be anchored in the TME. With continued efforts and advancements, we believe an increasing number of FNA-based fluorescence imaging probes will be utilized for TME imaging. This progress will significantly enhance our understanding of disease pathogenesis and progression, thereby offering substantial potential in biosensing and imaging analysis.

Detection of zearalenone by electrochemical aptasensor based on enzyme-assisted target recycling and DNAzyme release strategy

Zearalenone has a high level of detection and exceedance in cereals and by-products. Herein, an electrochemical aptasensor for ZEN detection was proposed. The selected aptamer, which has a high affinity for ZEN, serves as a molecular recognition element and effectively avoids interference from other toxins. Meanwhile, the strategy of exonuclease III-assisted target recycling and DNAzyme-catalysed substrate cleavage was combined. Aptamers and RNA-cleaving DNAzymes, two types of functional nucleic acids, have demonstrated considerable potential as key components of biosensors for the detection of biological targets. Enzyme-assisted signal amplification technology also helps to detect trace levels of ZEN. Under optimal conditions, the proposed aptasensor exhibited remarkable repeatability (RSD: 2.73 %) and superior detection performance over a wide concentration range (100 fg/mL-50 ng/mL), with a detection limit of 89 fg/mL. In actual analysis of cereal samples, the results are comparable to those of liquid chromatography, greatly extending the selectivity of ZEN detection.

Highly sensitive detection of the tetracycline resistance gene tetA in water supply systems with an autocatalytic deoxyribonucleic acid-based cascade circuit

Antibiotic resistance genes (ARGs)-contamination in water systems is a global concern, accelerating antimicrobial resistance and threatening public health, which demands an effective, low-cost and stable method for their on-site detection. Herein, we developed an innovative approach by combining the hybridization chain reaction (HCR) with deoxyribozymes to design an isothermal enzyme-free cascade initiator regenerating (IR) HCR-based amplification system. Minute quantities of targets can trigger exponentially amplified fluorescence signals through the self-catalytic feedback loop of the HCR mechanism. Tetracycline resistance genes (tetA) were specifically and sensitively detected with a remarkably low detection limit as low of 4.6 pM by introducing auxiliary hairpins. Furthermore, the adaptable nature of auxiliary hairpins enabled easy customization for detecting other ARGs by simply altering the recognition site, resulting in a high degree of specificity and versatility. The IR-HCR-based amplifier was used to analyze real water samples, and it was found that the detection results showed a good correlation with the detection results of ddPCR (R2=0.997), demonstrating its practical utility. The designed sensor operated in the absence of the polymerase chain reaction and accurately quantified the targets. It was sensitive and dependable for the on-site detection of ARGs within the environment and is expected to be broadly applied in environmental monitoring and detection. SYNOPSIS: This study developed an isothermal, enzyme-free cascade DNA circuit for the specific and sensitive detection of tetracycline resistance genes in aquatic environments. It provides valuable guidance for the on-site detection of antibiotic resistance genes without PCR technology.

Spatiotemporal dynamic and catalytically mediated reconfiguration of compartmentalized cyanuric acid/polyadenine DNA microdroplet condensates

Native cells possess membrane-bound subcompartments, organelles, such as mitochondria and lysosomes, that intercommunicate and regulate cellular functions. Extensive efforts are directed to develop synthetic cells, or protocells, that replicate these structures and functions. Among these approaches, phase-separated coacervate microdroplets composed of polymers, polysaccharides, proteins, or nucleic acids are gaining interest as cell-mimicking systems. Particularly, compartmentalization of the synthetic protocell assemblies and the integration of functional constituents in the containments allowing signaling, programmed transfer of chemical agents, and spatiotemporal controlled catalytic transformations across the protocell subdomains, are challenging goals in developing artificial cells. Here, we report the assembly of compartmentalized, phase-separated cyanuric acid/polyadenine coacervate microdroplets. Hierarchical, co-centric compartmentalization is achieved through the dynamic and competitive spatiotemporal occupation of pre-engineered barcode domains within the polyadenine microdroplet framework by invading DNA strands. By encoding structural and functional information within these DNA-invaded compartments, the light-triggered, switchable reconfiguration of compartments, switchable catalytic reconfiguration of containments, and reversible aggregation/deaggregation of the compartmentalized microdroplets are demonstrated.

Spatial Confinement of a Dual Activatable DNAzyme Sensor in the Cavity of a DNA Nanocage for Logic-Gated Molecular Imaging

Despite intense interest in design of DNAzyme sensors for molecular detection and imaging in living cells, their intracellular applications are still hampered by limited spatial control and poor bio-stability. Here we present controlled spatial confinement of a rationally designed, microRNA (miRNA)-activatable DNAzyme sensor probe (mDz) within the cavity of DNA nanocage, enabling efficient intracellular delivery with improved bio-stability for AND-gate molecular imaging. The mDz that possesses inactive DNAzyme activity is designed by the introduction of a blocking DNA strand, while miR-21 mediated strand displacement reaction allows for the formation of an intact DNAzyme structure for metal-ion-mediated catalytic reaction. Furthermore, the DNA nanocage serves as a nanocarrier for intracellular delivery of mDz, in which the cavity is accessible to the dual targets for logic-gated molecular imaging, while the confinement effect can provide steric protection of mDz by obstructing nuclease from entering the cavity of the DNA nanocage, resulting in enhanced bio-stability and improved molecular imaging precision. This strategy paves a way for the engineering of activatable DNA nanosensors with both self-delivery and self-protection capabilities to detect diverse intracellular targets.

Advancements in DNAzyme-based biosensors for the detection of hazardous substances in foodstuff: current applications and future perspectives

DNAzyme-based biosensors have emerged as a promising tool for ensuring food safety due to their high sensitivity, specificity, and potential for rapid, cost-effective detection of hazardous substances. These biosensors leverage DNAzymes-catalytically active DNA molecules-to detect a range of contaminants, including metal ions, fungal toxins, pesticides, and pathogens. While DNAzyme-based biosensors show significant advantages over conventional techniques, challenges such as nuclease degradation, interference from complex sample matrices, and the high costs associated with DNAzyme synthesis still hinder their widespread application. Recent advancements in the stability of DNAzymes, their immobilization strategies, and integration with nanomaterials are progressively addressing these limitations, enhancing the performance and reliability of DNAzyme-based sensors. This review highlights the structural and catalytic characteristics of DNAzymes, assesses their current applications in food safety, and discusses innovative strategies to overcome existing challenges. The continuous evolution of DNAzyme-based biosensors, particularly in design and device integration, holds great promise for their future role in routine, reliable food analysis.

Bioinspired Nucleic Acid-Based Bandpass Filters and Their Concentration-Adaptive Functions

Natural signaling networks can act as bandpass filters to interpret external stimuli within defined concentration ranges for differential cellular activities. Replicating such a bandpass filtering mechanism by synthetic networks poses a significant challenge. Herein, we introduce a modular design of nucleic acid-based multilayer threshold-gated incoherent feedforward networks as multiband bandpass filters to produce mutually exclusive responses within defined input concentration ranges. In these networks, nucleic acids demonstrate triple functionality by acting as threshold-gated entities to discern input concentration levels, serving as network nodes to assemble incoherent feedforward loops for nonlinear signal processing, and functioning as signal transduction units for coupling downstream functional modules. These modular networks enable the fine-tuning of filtering performance in terms of band position, bandwidth, cascades, and responses. A mathematical simulation model allows us to predict the filtering behaviors under various conditions. Also, the networks are integrated with upstream signal conversion modules to process concentration information on molecules beyond nucleic acids, such as adenosine and its derivatives. Furthermore, connections to downstream functional modules allow the system to regulate various processes in a concentration bandpass manner, realizing concentration-adaptive DNAzyme biocatalysis, tristate logic operations, RNA transcription, and DNA condensate formation. These findings underscore the potential of enzyme-free DNA reaction networks in complex signal processing and lay a solid foundation for developing chemical and material systems with highly adaptive and autonomous behaviors.

Biosensors and lateral flow immunoassays: Current state and future prospects

The advent of paper-based biosensors represents a novel paradigm in point-of-care (POC) diagnostics, emerging as versatile tools. However, the broad term "biosensors" can be misleading, encompassing a range of techniques such as dipstick assays, electrochemical, microfluidics and immunoassay-based biosensors (including lateral flow (LFA), vertical flow and nucleic acid-based immunoassays). This narrative review aims to consolidate the vast and dispersed information on biosensors into a systematically organized resource addressing both practical and theoretical aspects for researchers developing paper-based biosensors. It offers a comprehensive classification of biorecognition elements and labels, insights into various conjugation techniques, and characterization methods for both labels and conjugates. Following the development and optimization of biological reactions, this review emphasizes the careful selection of membranes and reagents to effectively reproduce molecular reactions on paper. Membranes are critical to biosensor efficacy, with fluid dynamics influenced by factors such as pore size, protein holding capacity and wicking rate. While POC diagnostics have traditionally provided binary (yes/no) results, advancements now allow for semi-quantitative and quantitative results. Technologies such as in-text, printers, various software's and smartphone can be used as colour analysis utilizing colour models beyond RGB like XYZ, grey intensity, CMY, CMYK, HSV and HSL that can analyse and process the colour intensity. AI integration further simplifies result analysis through image analysis, interpretation, predictive modelling, clinical decision support, enhancing detection, data integration and management. This review also emphasizes validation and stability studies in accordance with regulatory guidelines, ensuring the reliability of biosensors. The review ultimately covers: (i) A foundational understanding of various biosensor techniques, focusing on the self-sufficient LFA technique. (ii) Strategies to enhance sensitivity through pre- and post-assay modifications. (iii) A comprehensive troubleshooting section addressing common challenges in bioassay and fabrication. (iv) Multiplexing approaches enabling the simultaneous detection of multiple analytes for enhanced biomarker confirmation. By amalgamating knowledge from these approaches, this review offers the potential to elevate a basic traditional LFA strip into a highly sensitive diagnostic tool. It serves not only as a repository of knowledge but also as a roadmap for researchers and practitioners navigating the burgeoning field of paper-based biosensors.

A two-color fluorescence sensing strategy based on functionalized tetrahedral DNAzyme nanotweezers for ochratoxin A detection

A two-color fluorescent sensing strategy based on a functionalized tetrahedral DNAzyme nanotweezer (FTDN) was developed to detect ochratoxin A (OTA) utilizing the multifunctional properties of DNA nanotechnology. The FTDN enables rapid OTA detection directly through a Cy5 fluorescent group, modified to respond to the target signal. Additionally, FTDN exhibits DNAzyme cutting activity in the presence of Mg2⁺ ions, enabling it to traverse DNA nanoflower-functionalized magnetic beads. This process results in the continuous cleavage of DNA nanoflowers labeled with numerous FAM fluorescent groups, thereby amplifying the detection signal and enhancing OTA sensitivity. The linear ranges for the Cy5 and FAM signals in response to OTA were 5-1000 ng/mL and 0.05-100 ng/mL, respectively, with corresponding limits of detection (LOD) of 1.59 ng/mL and 0.03 ng/mL. This study demonstrates that dual-color fluorescence via Cy5 and FAM can effectively verify OTA detection in food, significantly reducing false-positive and false-negative rates. The proposed platform offers sensitive and accurate detection of mycotoxins in food and can be adapted for monitoring other trace contaminants by simply altering the aptamer.

Advances of functional nucleic acids based on specific recognition:A review

Nucleic acids, which are fundamental to living organisms, play a crucial role in carrying and transmitting genetic information. Advances in molecular biology have led to the exploration of functional nucleic acids (FNAs), including aptamers, DNAzymes, and G-quadruplexes, known for specific recognition or catalysis. FNAs with high specificity, sequence programmability, modification ease and biocompatibility, have extensive applications in biosensing, environmental monitoring, drug delivery and cancer diagnosis. This review focuses on the structure and specific recognition principles of FNAs, followed by an exploration for biosensing and biomedical applications, offering insights into current challenges and future trends in FNAs as recognition elements.

Fluorescent biosensor for lead ion detection based on GR-5 DNAzyme and self-hybridization chain reaction

BACKGROUND

Lead ion (Pb2+) is a typical heavy metal pollutant, and the water and food contaminated by lead may pose a potential threat to the environment and human health. In the natural environment, it can accumulate in soil and water, affecting the entire food chain. For human health, even if the Pb2+ content is very low, it can cause a series of adverse health effects. In order to effectively address the issue of lead pollution, it is particularly important to develop highly sensitive and selective Pb2+ detection technology.

RESULTS

In this study, we designed a single-hairpin based self-hybridization chain reaction (SHCR) system for Pb2+ detection based on GR-5 DNAzyme. Compared with the traditional hybridization chain reaction (HCR) which requires two hairpins, this strategy only needs one hairpin probe, this design not only reduces the experimental cost, but also simplifies the sequence design and experimental operation. Once Pb2+ was added in the system, GR-5 DNAzyme can be actived and then a trigger DNA was released to trigger the SHCR reaction, thereby a signal-amplified fluorescent biosensor for Pb2+ detection was developed, which exhibited a good linear range from 100 to 500 nM with a low detection limit of 24.8 nM, and has been successfully applied to the determination of Pb2+ in environmental water and Chinese Baijiu.

SIGNIFICANCE

This simple, sensitive, and selective Pb2+ detection system demonstrates significant potential for a wide range of practical applications in both environment and food monitoring. In addition to its specific application for Pb2+ detection, by introducing different DNAzymes, this SHCR system can be applied for the detection of other heavy metal ions.

Programmable Split DNAzyme Modulators via Allosteric Cooperative Activation for mRNA Electrochemiluminescence Biosensing

DNAzymes, known for their programmability, stability, and cost-effectiveness, are powerful tools for signal transduction in complex biological systems. However, their application in responding to target effectors is often hindered by limited catalytic efficiency and susceptibility to unintended activation. Here we propose an allosteric cooperative activation strategy to program a split DNAzyme modulator (STATER) that enables sensitive and accurate electrochemiluminescence (ECL) biosensing of interleukin-6 (IL-6) mRNA. Our design features a STATER that leverages a DNA tetrahedron as a central scaffold, equipped with two pairs of T-shaped hairpin probes (TP) and helper hairpin probes (HP). Specifically, the TP contains two apurinic/apyrimidinic endonuclease 1 (APE1) recognition sites, an IL-6 mRNA recognition region, and a partzyme fragment, while the HP contains a corresponding paired partzyme fragment. Unlike conventional DNAzyme modulators that rely on single effector activation, the STATER integrates an allosteric cooperative activation mechanism, which ensures that all preblocked components are synergistically activated and assembled within a confined space, facilitating rapid and specific reconstruction of the DNAzyme's catalytic active domain. Furthermore, upon cooperative recognition by APE1 and IL-6 mRNA, two inactive partzymes undergo an allosteric assembly via a toehold exchange displacement reaction, switching on the cleavage reactivity of STATER. This mechanism enables the establishment of an activation threshold for IL-6 mRNA, thereby minimizing nonspecific activation in complex scenarios. Our studies demonstrate that the STATER exhibits outstanding sensitivity and selectivity for IL-6 mRNA detection using the supramolecular gold nanoclusters network-based ECL platform. The biosensor provides a linear detection span from 1 × 10-13 to 1 × 10-7 M, with a limit of detection as low as 3.26 × 10-14 M, highlighting STATER's potential for detecting various analytes in complex biological systems.

Nucleic Acid Drugs in Radiotherapy

Radiotherapy remains a cornerstone of cancer treatment, using high-energy radiation to induce DNA damage in tumor cells, leading to cell death. However, its efficacy is often hindered by challenges such as radiation resistance and side effects. As a powerful class of functional molecules, nucleic acid drugs (NADs) present a promising solution to these limitations. Engineered to target key pathways like DNA repair and tumor hypoxia, NADs can enhance radiotherapy sensitivity. NADs can also serve as delivery vehicles for radiotherapy agents such as radionuclides, improving targeting accuracy and minimizing side effects. This review explores the role of NADs in optimizing radiotherapy, highlighting their mechanisms, clinical applications, and synergies with radiotherapy, ultimately offering a promising strategy for improving patient outcomes in cancer therapy.

Luminescent Lanthanides in Biorelated Applications: From Molecules to Nanoparticles and Diagnostic Probes to Therapeutics

Lanthanides are particularly effective in their clinical applications in magnetic resonance imaging and diagnostic assays. They have open-shell 4f electrons that give rise to characteristic narrow, line-like emission which is unique from other fluorescent probes in biological systems. Lanthanide luminescence signal offers selection of detection pathways based on the choice of the ion from the visible to the near-infrared with long luminescence lifetimes that lend themselves to time-resolved measurements for optical multiplexing detection schemes and novel bioimaging applications. The delivery of lanthanide agents in cells allows localized bioresponsive activity for novel therapies. Detection in the near-infrared region of the spectrum coupled with technological advances in microscopies opens new avenues for deep-tissue imaging and surgical interventions. This review focuses on the different ways in which lanthanide luminescence can be exploited in nucleic acid and enzyme detection, anion recognition, cellular imaging, tissue imaging, and photoinduced therapeutic applications. We have focused on the hierarchy of designs that include luminescent lanthanides as probes in biology considering coordination complexes, multimetallic lanthanide systems to metal-organic frameworks and nanoparticles highlighting the different strategies in downshifting, and upconversion revealing some of the opportunities and challenges that offer potential for further development in the field.

Endogenous HClO-Gated Cascade MicroRNA Imaging for Precise Diagnosis of Atherosclerosis In Vivo

Precise imaging of atherosclerotic plaques using biomarkers could prompt the diagnosis and clinical management of atherosclerosis (AS)-driven cardiovascular diseases. MicroRNA-155 (miR-155) plays a critical role in AS development, with its expression notably upregulated in foam cells within plaques. However, miRNA imaging methods for atherosclerotic plaques face significant challenges, including low specificity, inefficient delivery, and poor cell selectivity. Herein, we develop an endogenous hypochlorous acid (HClO)-gated cascade signal amplification strategy for precise miR-155 imaging in living foam cells, enabling accurate in vivo and ex vivo detection of atherosclerotic plaques. This strategy utilizes a phosphorothioate (PT)-modified hairpin probe that is specifically deprotected by HClO and uncaged by miR-155, triggering a catalytic hairpin assembly (CHA) to amplify fluorescence signals. The PT-CHA probes are encapsulated in lipid nanoparticles (LNs), followed by conjugating with phosphatidylserine (PS)-binding peptide (PBP) for selectively targeting foam cells, enabling in vivo miR-155 imaging in atherosclerotic plaques. The fluorescence intensity of PT-CHA@LN-PBP in the aorta region shows clear differentiation among AS-bearing mice, miR-155-/- mice, and healthy mice. Moreover, the fluorescence intensity strongly correlates with plaque area and AS progression and can discriminate plaque vulnerability risk with an area under the curve (AUC) of 0.94. Imaging of human aortic tissues further validates the probe's capacity to distinguish atherosclerotic plaques from normal endarterium. These findings establish PT-CHA@LN-PBP as a noninvasive, reliable diagnostic tool for precise assessment of AS.

Highly Sensitive and Selective Detection of Uranyl Ions Based on a Tb3+-Functionalized MOF via Competitive Host-Guest Coordination

Owing to the rapid development of the nuclear industry, uranium has become a global environmental contaminant due to its radiotoxicity and chemotoxicity, posing significant threats to human health and ecological safety. Although various instrumental and chemical analytical methods have been developed for uranyl ion detection in aquatic environments, searching for new sensors with high stability, sensitivity, and selectivity remains a challenge. In this study, a luminescent Zr-based metal-organic framework (MOF), designated as Tb@UiO-66-(COOH)2, was successfully synthesized utilizing a postsynthetic exchange (PSE) method along with Tb3+ ion doping for uranyl ion detection. Interestingly, the presence of UO22+ ions causes a replacement of guest ions (Tb3+) in the sensor via a competitive host-guest interaction, leading to significant luminescence quenching. The attenuation of the luminescence intensity of Tb@UiO-66-(COOH)2 exhibits an excellent linear relationship with UO22+ ion concentrations within a wide range of 0-2.52 μM. Notably, Tb@UiO-66-(COOH)2 demonstrates an unprecedentedly high detection sensitivity (Ksv = 2.16 × 105 M-1) and an extremely low limit of detection (LOD) down to 8.03 nM (1.91 ppb) in deionized water. More importantly, Tb@UiO-66-(COOH)2 can achieve high selectivity and efficient detection performance, even in the presence of significant excesses of competing ions. The values of Ksv were determined to be 2.10 × 105 M-1 in Xie'ao Lake water and 3.05 × 105 M-1 in seawater; the values of LOD were determined to be 8.26 nM (1.96 ppb) in Xie'ao Lake water and 5.68 nM (1.35 ppb) in seawater. To the best of our knowledge, this is the first instance of introducing a competitive host-guest coordination strategy into a MOF-based chemical sensor to achieve high-performance uranyl ion detection. Hence, the present work offers a novel idea for building functional MOFs for uranyl ion detection in aqueous solutions.

Exploration and Application of the Catalytic Superiority of Non-G-Quadruplex Hemin Aptamers

A newly identified hemin aptamer with a non-G-quadruplex structure exhibits stronger peroxidase activity and selectivity than traditional G-quadruplex/hemin DNAzymes, addressing challenges such as weak hemin binding, low catalytic activity, and poor selectivity. In this study, we optimized ion activation conditions, refined reaction parameters, and developed a spontaneous recombination method via aptamer splitting to enhance DNAzyme activity and enable activity regulation. The aptamer demonstrated superior performance in enzyme-free sensing, polymerase-assisted amplification, and CRISPR/Cas12a systems, achieving higher sensitivity and improved colorimetric thresholds compared to G-quadruplexes. We have also developed a comprehensive operational guide for aptamer/hemin DNAzymes, which is poised to revolutionize colorimetric sensor signal generation elements.

Chemical Engineering of DNAzyme for Effective Biosensing and Gene Therapy

RNA-cleaving DNAzymes are in vitro selected functional nucleic acids with inherent catalytic activities. Due to their unique properties, such as high specificity, substrate cleavage capability, and programmability, DNAzymes have emerged as powerful tools in the fields of analytical chemistry, chemical biology, and biomedicine. Nevertheless, the biological applications of DNAzymes are still impeded by several challenges, such as structural instability, compromised catalytic activity in biological environments and the lack of spatiotemporal control designs, which may result in false-positive signals, limited efficacy or non-specific activation associated with side effects. To address these challenges, various strategies have been explored to regulate DNAzyme activity through chemical modifications, enhancing their stability, selectivity, and functionality, thereby positioning them as ideal candidates for biological applications. In this review, a comprehensive overview of chemically modified DNAzymes is provided, discussing modification strategies and the effects of these modifications on DNAzymes. Specific examples of the use of chemically modified DNAzymes in biosensing and gene therapy are also presented and discussed. Finally, the current challenges in the field are addressed and offer perspectives on the potential direction for chemically modified DNAzymes.

Sensitive detection of FPG based on 8-oxoG modified chimeric peptide-DNA enzyme for oxidative damage evaluation

Formamidopyrimidine DNA glycosylase (FPG) is a crucial DNA repair enzyme that specifically recognizes and excises the damaged base 7,8-dihydro-8-oxoguanine (8-oxoG). The current detection technology for FPG is limited due to the need of integrating the relatively independent identification components and signal amplifiers. Herein, we designed an integrated probe (loaded on magnetic beads), which contained 8-oxoG for FPG recognition and a novel chimeric peptide-DNA mimetic enzyme (CPDzyme) for chemiluminescence (CL) signal amplification. Once the FPG recognized the probe, the CPDzyme was excised from the surface of the magnetic beads. Therefore, the change in CL signal caused by CPDzyme on the surface of the magnetic spheres before and after recognition and cleaning could be quantitatively analyzed for FPG. Thanks to the powerful catalytic ability of CPDzyme and the simplicity of the CL system, this method could detect the activity of FPG in a linear range of 0.2-20 U/mL, with the detection limit as low as 0.06 U/mL. Further, we applied the strategy to the detection of FPG activity in human serum and bacterial samples (before and after UV irradiation), demonstrating its potential for the monitoring of oxidative damage. With excellent sensitivity and standardized operation, this strategy demonstrates superior characteristics to commercial assay kits and is expected to provide a new powerful tool for relevant research.

A review towards sustainable analyte detection: Biomimetic inspiration in biosensor technology

The branch of biomimetics has witnessed a profound impact on the field of biosensor technology, reflected in sustainable analyte detection. A vast array of biosensor platforms with improved/upgraded performance have been developed and reported. No wonder the motivation from the field of biomimetics has a huge impact on generating detection systems with escalated degrees of manipulation and tunability at different levels. More recently, biomimetic biosensor technology has found potential in constructing bio-inspired materials such as aptamers, MIPs, nanozymes, DNAzymes, Synzymes, etc. to be integrated with biosensor fabrication. The establishment of a sensing setup is not limited to the bioreceptor fabrication; the construction of transducing element using biomimetic material have been reported too. Moreover, to serve a biosensing of target analyte from a fatal diseased sample different biomimetic architectures can be designed that mimic in-vivo microenvironmental surroundings to get an exact microenvironment equivalent to natural conditions leading towards designing of a precise treatment strategy. This research area is ever-evolving as there is a scope for upgradation and refinement due to advancing technologies including nanotechnology, biomimetic nanomaterials, microfluidics, optical sensors, etc. This review is an attempt to comprehend and juxtapose the very primary innovations in the field of biomimetic biosensor technology to realize its comprehensive and wide-range scope and possibilities.

Construction of a hierarchical DNA circuit for single-molecule profiling of locus-specific N6-methyladenosine-MALAT1 in clinical tissues

N6-methyladenosine (m6A) is the most important internal methylation in eukaryotic RNAs, and it is critically implicated in diverse RNA metabolisms for cancer development. Because epigenetic modifications do not interfere with Watson-Crick base pairing and m6A modification is not susceptible to chemical decorations, standard hybridization-based techniques cannot be applied for sensing m6A in RNAs. Consequently, the development of new methods for accurate and sensitive profiling of locus-specific m6A in RNAs remains a great challenge. Herein, we demonstrate for the first time the construction of a hierarchical DNA circuit for single-molecule profiling of locus-specific m6A-metastasis-associated lung adenocarcinoma transcript 1 (m6A-MALAT1) in clinical tissues. Taking advantage of high discrimination of VMC10-DNAzyme between m6A and A, exponential efficiency of hierarchical DNA circuit, and ultrahigh signal-to-noise ratio of single-molecule detection, this nanodevice exhibits attomolar sensitivity with a limit of detection (LOD) of 1.8 aM for m6A-MALAT1 in vitro and a dynamic range of 7 orders of magnitude. Moreover, it can discriminate 0.001% m6A-MALAT1 from excess A-MALAT1, quantify m6A-MALAT1 in diverse cancer cells at single-cell level, distinguish m6A-MALAT1 expressions in breast cancer patients and healthy individuals, and monitor cellular m6A-MALAT1 for gene therapy, offering a promising platform for epitranscriptomic research and clinical diagnostics.

Spherical DNA Nanomotors Enable Ultrasensitive Detection of Active Enzymes in Extracellular Vesicles for Cancer Diagnosis

Enzymes encapsulated in extracellular vesicles (EVs) hold promise as biomarkers for early cancer diagnosis. However, precise measurement of their catalytic activities within EVs remains a notable challenge. Here, we report an enzymatically triggered spherical DNA nanomotor (EDM) that enables one-pot, cascaded, and highly sensitive analysis of the activity of EV-associated or free apurinic/apyrimidinic endonuclease 1 (APE1, a key enzyme in base excision repair) across various biological samples. The EDM capitalizes on APE1-triggered activation of DNAzyme (Dz) and its autonomous cleavage of substrates to achieve nonlinear signal amplification. Using EDM, we demonstrate a strong correlation between APE1 activity in EVs and that of their parental cancer cells. Additionally, EV APE1 mirrors the fluctuation of cellular APE1 activity in response to chemotherapy-induced DNA damage. In a pilot clinical study (n=63), the EDM-based assay reveals that more than 80 % of active APE1 in serum samples is EV-encapsulated. Notably, EV APE1 can differentiate early prostate cancer (PCa) patients from healthy donors (HDs) with an overall accuracy of 92 %, outperforming free APE1 in sera. We anticipate that EDM will become a versatile tool for quantifying EV-associated enzymes.

Host-guest recognition-mediated reversible and orthogonal regulation of DNAzyme activity

The host-guest recognition system is incorporated into the core region of the 10-23 DNAzyme for precise regulation of its functionality. Biochemical experiments demonstrate reversible and orthogonal control of the DNAzyme function using cucurbit(7)uril and its competitive guests. Furthermore, cellular experiments indicate the gene expression can be effectively manipulated through this ligand-controllable DNAzyme.

DNAzyme assisted single amplification for FEN1 activity detection using a personal glucose meter

Flap endonuclease 1 (FEN1) plays a vital role in cancer by modulating DNA repair mechanisms, inducing genomic instability, and serving as a promising biomarker for cancer diagnosis and prognosis. In this work, we present the development of a novel DNAzyme signal amplification-directed point-of-care sensing system (Dz-PGM) for the sensitive and specific detection of FEN1. The Dz-PGM system utilizes DNAzyme signal amplification in conjunction with a personal glucose meter (PGM) for reporting, capitalizing on a biochemical cascade initiated by FEN1 recognition. Benefiting from enzymatic recognition, magnetic separation, and DNAzyme based signal amplification, this Dz-PGM system demonstrates exceptional specificity and achieves a low detection limit of 3.56× 10-2 U/mL for FEN1. The versatility of the system is further demonstrated through its ability to screen FEN1 inhibitor drugs and to distinguish FEN1 levels in real cell samples with high accuracy. The article underscores the potential of the Dz-PGM system as a promising tool for early cancer diagnosis, and in constructing sensitive detection platforms for DNA repair enzymes.

Subcellular Compartment-Specific Amplified Imaging of Metal Ions via Ribosomal RNA-Regulated DNAzyme Sensors

Although DNAzyme sensors have been widely developed for imaging metal ions, their application in specific subcellular compartments remains challenging due to low spatial controllability. Here we present a locally activatable, DNAzyme-based sensing technology that enables subcellular compartment-specific imaging of metal ions through ribosomal RNA (rRNA) regulated signal amplification. The system leverages a subcellularly encoded rRNA to locally activate DNAzyme-based sensors, and further drives signal amplification via multiple turnover cleavage of molecular beacons, to significantly enhance sensitivity and spatial precision for metal-ion imaging in specific organelles (e.g. mitochondria) or membraneless compartments (e.g. cytosol). Furthermore, we demonstrate that the system allows in situ monitoring of subcellular dynamics of mitochondrial Zn2+ during ischemia and the drug intervention. This study expands the DNAzyme toolbox for investigating the role of subcellular metal-ion dynamics in disease processes.

Aptamer and DNAzyme Based Colorimetric Biosensors for Pathogen Detection

The detection of pathogens is critical for preventing and controlling health hazards across clinical, environmental, and food safety sectors. Functional nucleic acids (FNAs), such as aptamers and DNAzymes, have emerged as versatile molecular tools for pathogen detection due to their high specificity and affinity. This review focuses on the in vitro selection of FNAs for pathogens, with emphasis on the selection of aptamers for specific biomarkers and intact pathogens, including bacteria and viruses. Additionally, the selection of DNAzymes for bacterial detection is discussed. The integration of these FNAs into colorimetric biosensors has enabled the development of simple, cost-effective diagnostic platforms. Both non-catalytic and catalytic colorimetric biosensors are explored, including those based on gold nanoparticles, polydiacetylenes, protein enzymes, G-quadruplexes, and nanozymes. These biosensors offer visible detection through color changes, making them ideal for point-of-care diagnostics. The review concludes by highlighting current challenges and future perspectives for advancing FNA-based colorimetric biosensing technologies for pathogen detection.

MicroRNA-Triggered Programmable DNA-Encoded Pre-PROTACs for Cell-Selective and Controlled Protein Degradation

Proteolysis-targeting chimeras (PROTACs) have accelerated drug development; however, some challenges still exist owing to their lack of tumor selectivity and on-demand protein degradation. Here, we developed a miRNA-initiated assembled pre-PROTAC (miRiaTAC) platform that enables the on-demand activation and termination of target degradation in a cell type-specific manner. Using miRNA-21 as a model, we engineered DNA hairpins labeled with JQ-1 and pomalidomide and facilitated the modular assembly of DNA-encoded pre-PROTACs through a hybridization chain reaction. This configuration promoted the selective polyubiquitination and degradation of BRD4 upon miR-21 initiation, highlighting significant tumor selectivity and minimal systemic toxicity. Furthermore, the platform incorporates photolabile groups, enabling the precise optical control of pre-PROTACs during DNA assembly/disassembly, mitigating the risk of excessive protein degradation. Additionally, by introducing a secondary ligand targeting CDK6, these pre-PROTACs were used as a modular scaffold for the programmable assembly of active miRiaTACs containing two different warheads in exact stoichiometry, enabling orthogonal multitarget degradation. The integration of near-infrared light-mediated photodynamic therapy through an upconversion nanosystem further enhanced the efficacy of the platform with potent in vivo anticancer activity. We anticipate that miRiaTAC represents a significant intersection between dynamic DNA nanotechnology and PROTAC, potentially expanding the versatility of PROTAC toolkit for cancer therapy.

Ultrasensitive detection of cancer-associated nucleic acids and mutations by primer exchange reaction-based signal amplification and flow cytometry

The detection of cancer-associated nucleic acids and mutations through liquid biopsy has emerged as a highly promising non-invasive approach for early cancer detection and monitoring. In this study, we report the development of primer exchange reaction (PER) based signal amplification strategy that enables the rapid, sensitive and specific detection of nucleic acids bearing cancer specific single nucleotide mutations using flow cytometry. Using micrometer size beads as support for immobilizing oligonucleotides and programmable PER assembly for target oligonucleotide recognition and fluorescence signal amplification, we demonstrated the versatile detection of target nucleic acids including KRAS oligonucleotide, fragmented mRNAs, and miR-21. Moreover, our detection system can discriminate single base mutations frequently occurred in cancer-associated genes including KRAS, PIK3CA and P53 from cell extracts and circulating tumor DNAs (ctDNAs). The detection is highly sensitive, with a limit of detection down to 27 fM without pre-amplification. In view of a clinical application, we demonstrate the detection of single mutations after extraction and pre-amplification of ctDNAs from the plasma of breast cancer patients. Importantly, our detection strategy enabled the detection of single KRAS mutation even in the presence of 1000-fold excess of wild type (WT) DNA using multi-color flow cytometry detection approach. Overall, our strategy holds immense potential for clinical applications, offering significant improvements for early cancer detection and monitoring.

Effective multicolor visual biosensor for ochratoxin A detection enabled by DNAzyme catalysis and gold nanorod etching

A novel detection technique is introduced that offers sensitive and reliable ochratoxin A (OTA) detection. The method leverages the etching of gold nanorods (AuNRs) stabilized by hexadecyl trimethyl ammonium bromide (CTAB) using the oxidized form of 3,3',5,5'-tetramethyl benzidine sulfate (TMB2+), creating a susceptible multicolor visual detection system for OTA. The visual detection is enabled by Mg2+-assisted DNAzyme catalysis combined with the catalytic hairpin assembly (CHA) signal amplification strategy. The presence of OTA triggers CHA and signaling responses along with the formation of G-quadruplex-hemin DNAzyme, which promotes the oxidation of TMB with H2O2, leading to the etching of AuNRs and a reduction in their aspect ratio. AuNRs experienced a blue shift in the longitudinal localized surface plasmon resonance peak, resulting in a color change. The technique has been shown to detect OTA with a low detection limit of 0.309 pg/mL, demonstrating high sensitivity and specificity. The detection technique offers versatility by enabling the detection of other pollutants through a simple replacement of the aptamer, expanding the range of detection platforms available for pollutant determinations.

Engineering a Near-Infrared Spiro-Based Aggregation-Induced Emission Luminogen for DNAzyme-Sensitized Photothermal Therapy with High Efficiency and Accuracy

Aggregation-induced emission luminogen (AIEgens)-based photothermal therapy (PTT) has grown into a sparkling frontier for tumor ablation. However, challenges remain due to the uncoordinated photoluminescence (PL) and photothermal properties of classical AIEgens, along with hyperthermia-induced antiapoptotic responses in tumor cells, hindering satisfactory therapeutic outcomes. Herein, a near-infrared (NIR) spiro-AIEgen TTQ-SA was designed for boosted PTT by auxiliary DNAzyme-regulated tumor cell sensitization. TTQ-SA with a unique molecular structure and packing mode was initially fabricated, endowing it with a strong AIE effect, favorable PL quantum yield, and good photothermal performance. DNAzyme, as a gene silencing tool, could alleviate antiapoptosis response during PTT. By integrating TTQ-SA and DNAzyme into folate-modified poly(lactic-co-glycolic acid) (PLGA) polymer, the as-fabricated nanosystem could promote cell apoptosis and sensitize tumor cells to PTT, thereby maximizing the therapeutic outcomes. With the combination of spiro-AIEgen-based PTT and DNAzyme-based gene silencing, the as-designed nanosystem showed promising NIR and photothermal imaging abilities for tumor targeting and demonstrated significant cell apoptotic, antitumor, and antimetastasis effects against orthotopic breast cancer. Furthermore, a synergistic antitumor effect was realized in spontaneous MMTV-PyMT transgenic mice. These findings offer new insights into AIEgen-based photothermal theranostics and DNAzyme-regulated tumor cell sensitization, paving the way for synergistic gene silencing-PTT nanoplatforms in clinical research.

A sensitive tobramycin electrochemical aptasensor based on multiple signal amplification cascades

The residue of tobramycin, a broad spectrum antibiotic commonly used in animal husbandry, has evitable impact on human health, which may cause kidney damage, respiratory paralysis, neuromuscular blockade and cross-allergy in humans. Sensitive monitoring of tobramycin in animal-derived food products is therefore of great importance. Herein, a new aptamer electrochemical biosensor for sensing tobramycin with high sensitivity is demonstrated via exonuclease III (Exo III) and metal ion-dependent DNAzyme recycling and hybridization chain reaction (HCR) signal amplification cascades. Tobramycin analyte binds aptamer-containing hairpin probe to switch its conformation to expose the toehold sequence, which triggers Exo III-based catalytic digestion of the secondary hairpin to release many DNAzyme strands. The substrate hairpins immobilized on the Au electrode (AuE) are then cyclically cleaved by the DNAzymes to form ssDNAs, which further initiate HCR formation of lots of long methylene blue (MB)-tagged dsDNA polymers on the AuE. Subsequently electro-oxidation of these MB labels thus exhibit highly enhanced currents for sensing tobramycin within the 5-1000 nM concentration range with an impressive detection limit of 3.51 nM. Furthermore, this strategy has high selectivity for detecting tobramycin in milk and shows promising potential for detect other antibiotics for food safety monitoring.

A DNAzyme-Based Nanohybrid for Ultrasound and Enzyme Dual-Controlled mRNA Regulation and Combined Tumor Treatment

Despite the significant potential of RNA-cleaving DNAzymes for gene regulation, their application is limited by low therapeutic efficacy and lack of cell-specific control. Here, a DNAzyme-based nanohybrid designed for ultrasound (US)-controlled, enzyme-activatable mRNA regulation is presented, enabling tumor cell-selective combination therapy. The nanohybrid is constructed by coordination-directed self-assembly of an enzymatically-triggerable therapeutic DNAzyme (En-Dz) and natural sonosensitizer hemoglobin (Hb). Controlled US exposure induces reactive oxygen species generation from Hb units, which not only facilitates efficient endosomal escape of En-Dz, but also promotes the translocation of specific enzyme from the nucleus to the cytoplasm, thereby enhancing gene regulation efficacy. Notably, the enzyme-triggered, spatiotemporally-controlled activation of En-Dz's catalytic activity results in enhanced cancer-cell selectivity in the therapeutic treatment. Furthermore, the combination of enzyme-activated mRNA regulation and sonodynamic therapy significantly enhances anti-tumor efficacy both in vitro and in vivo. This work highlights the potential of integrating a sonodynamic strategy to overcome the current limitations of DNAzyme-based gene regulators, providing a spatiotemporally-controlled approach for precise tumor treatment.

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.

DNA Conformation-Regulated Hemin Switch for Lab-on-Chip Chemiluminescent Detection of an Antibody Secreted from Hybridoma Cells

This work designed a DNA conformation-regulated hemin switch for rapid chemiluminescent (CL) detection of a monoclonal antibodies. This switch was performed with an affinity probe and an inhibition probe, which were conveniently prepared by hybridizing hemin-labeled DNA1 with KHL peptide-labeled DNA2 and binding biotin-labeled DNA3 to streptavidin, respectively. In the absence of the target antibody, streptavidin-DNA3 could hybridize with hemin-DNA1/KHL-DNA2 to release KHL-DNA2, which led to the loss of hemin activity due to the affinity hindrance of streptavidin-DNA3. After the KHL peptide was recognized by the target antibody, the strand replacement hybridization could be inhibited by the bound antibody, which retained the high catalytic activity of hemin overhung on the antibody-bound affinity probe for a CL reaction, leading to a "signal-on" process for CL antibody detection. Using a KHL-specific antibody, anti-proprotein convertase subtilisin/kexin type 9 antibody (PCSK9-Ab), as a target model and common L012-1,2,4-triazole-H2O2 CL system, the designed switch showed a detection range of 10 ng mL-1 to 1 μg mL-1 with a detection limit of 4.16 ng mL-1 (56.2 pM) and a short analytical time of 6.5 min. The proposed quick method could simply be used for lab-on-chip CL detection of PCSK9-Ab in situ-secreted from PCSK9-6E3 hybridoma cells, which showed an accuracy of 90.2% compared with the statistical results from general fluorescence imaging, providing a potential technique for screening specific hybridoma cells.

A close-looped DNAzyme walker with an available catalytic domain for electrochemiluminescent detection of acetamiprid

Traditional DNA walkers face enormous challenges due to limited biostability and reaction kinetics. Herein, we designed a self-driven close-looped DNAzyme walker (cl-DW) with high structural biostability and catalytic activity that enabled rapid electrochemiluminescence (ECL) detection of pesticide residue acetamiprid. Specifically, cl-DW exhibited increasing ability to resist nuclease degradation with a 570-fold longer half-degradation time than that of the single-stranded DNAzyme walker (ss-DW) due to the protected DNA terminal. Furthermore, cl-DW achieved high catalytic activity with a 4.3-fold faster reaction kinetic than that of ss-DW due to the circularized nanostructure of an available catalytic domain. Consequently, we utilized cl-DW as a signal amplifier and tin-based sulfide (SnS2) nanoflowers as ECL emitters to construct an ECL aptasensor, which realized the sensitive detection of acetamiprid with a limit of detection of 0.85 nM. This work provides a reliable approach to exploring DNA walkers with high catalytic activity and better biostability for molecular monitoring.

Enhanced Detection of Vibrio harveyi Using a Dual-Composite DNAzyme-Based Biosensor

Vibrio harveyi is a serious bacterial pathogen which can infect a wide range of marine organisms, such as marine fish, invertebrates, and shrimp, in aquaculture, causing severe losses. In addition, V. harveyi can be transmitted through food and water, infecting humans and posing a serious threat to public safety. Therefore, rapid and accurate detection of this pathogen is key for the prevention and control of related diseases. In this study, nine rounds of in vitro screening were conducted with Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology using unmodified DNA libraries, targeting the crude extracellular matrix (CEM) of V. harveyi. Two DNAzymes, named DVh1 and DVh3, with high activity and specificity were obtained. Furthermore, a fluorescent biosensor with dual DNAzymes was constructed which exhibited improved detection efficiency. The sensor showed a good fluorescence response to multiple aquatic products (i.e., fish, shrimp, and shellfish) infected with V. harveyi, with a detection limit below 11 CFU/mL. The fluorescence signal was observed within 30 min of reaction after target addition. This simple, inexpensive, highly effective, and easy to operate DNAzymes biosensor can be used for field detection of V. harveyi.

Autocatalytic DNA circuitries

Autocatalysis, a self-sustained replication process where at least one of the products functions as a catalyst, plays a pivotal role in life's evolution, from genome duplication to the emergence of autocatalytic subnetworks in cell division and metabolism. Leveraging their programmability, controllability, and rich functionalities, DNA molecules have become a cornerstone for engineering autocatalytic circuits, driving diverse technological applications. In this tutorial review, we offer a comprehensive survey of recent advances in engineering autocatalytic DNA circuits and their practical implementations. We delve into the fundamental principles underlying the construction of these circuits, highlighting their reliance on DNAzyme biocatalysis, enzymatic catalysis, and dynamic hybridization assembly. The discussed autocatalytic DNA circuitry techniques have revolutionized ultrasensitive sensing of biologically significant molecules, encompassing genomic DNAs, RNAs, viruses, and proteins. Furthermore, the amplicons produced by these circuits serve as building blocks for higher-order DNA nanostructures, facilitating biomimetic behaviors such as high-performance intracellular bioimaging and precise algorithmic assembly. We summarize these applications and extensively address the current challenges, potential solutions, and future trajectories of autocatalytic DNA circuits. This review promises novel insights into the advancement and practical utilization of autocatalytic DNA circuits across bioanalysis, biomedicine, and biomimetics.

A target-triggered colorimetric sensor for ultrasensitive detection of miRNAs based on self-powered three-dimensional DNA walker

MicroRNAs (miRNAs) play an important role in the process of heart failure (HF) and are emerging biomarkers that can be used for the auxiliary diagnosis of HF. However, it is very challenging to accurately analyze the expression levels of trace miRNAs in complex clinical samples. Here, we developed an enzyme-free colorimetric sensor for the ultrasensitive detection of miRNA-423-5p (HF-associated miRNA) based on three-dimensional DNA walkers constructed from functional nucleic acids and gold nanoparticles (AuNPs). DNAzyme with cleavage activity was specifically activated by miRNA-423-5p to sustainably cleave the substrate, thereby releasing the trigger sequence to initiate the subsequent mismatched catalytic hairpin assembly (MCHA) cycle. Then, as the MCHA cycle proceeded to continuously expose the G-quadruplex (GQ) sequence, the sequence bound with hemin to form a large amount of GQ/hemin DNAzyme on the surface of the AuNPs, which rapidly catalyzed the chromogenic oxidation of 3,3',5,5'-tetramethylbenzidine to yield an amplified colorimetric signal readout. The colorimetric sensor exhibited an ultralow detection limit (32 fM), showed excellent specificity and performed well in serum samples. The sensor was applied to detect miRNA-423-5p in clinical plasma samples from healthy individuals and HF patients, and the results revealed its good clinical application in HF diagnosis. Thus, the developed colorimetric sensor provides a convenient detection tool for early screening and diagnosis of HF, as well as for pathophysiological studies.

Fluorescence assay for aflatoxin B1 based on aptamer-binding triggered DNAzyme activity

As a kind of mycotoxin, aflatoxin B1 (AFB1), which is often found in agricultural products, poses a threat to human health. Developing a simple sensitive method for AFB1 detection is in great demand. Here, we reported an aptamer-based fluorescence assay for AFB1 detection by using DNAzyme to generate and amplify a signal. We redesigned a pair of DNA sequences, which originated from the anti-AFB1 aptamer and RNA-cleaving DNAzyme 10-23. In the absence of AFB1, the aptamer hybridized with the region of the substrate-binding arm of the DNAzyme, inhibiting the activity of the DNAzyme. In the presence of AFB1, the binding of AFB1 to the aptamer led to the displacement of the DNAzyme from the aptamer. The substrate-binding arm was unblocked, and the activity of the DNAzyme was restored for the hydrolysis of the fluorophore and quencher-labeled substrate, causing a significant fluorescence increase. This assay could detect AFB1 in the dynamic range from 0.98 to 2000 nmol/L with high selectivity, and the detection limit was 0.98 nmol/L. Moreover, the assay was able to detect AFB1 in a complex sample matrix. This work provides a useful tool for the analysis of AFB1.

Fusing Allosteric Ribozymes with CRISPR-Cas12a for Efficient Diagnostics of Small Molecule Targets

The CRISPR-Cas systems are adopted as powerful molecular tools for not only genetic manipulation but also point-of-care diagnostics. However, methods to enable diagnostics of non-nucleic-acid targets with these systems are still limited. Herein, by fusing ligand-dependent allosteric ribozymes with CRISPR-Cas12a, a derived CRISPR-Cas system is created for efficient quantitative analysis of non-nucleic-acid targets in 1-2 h. On two different small molecules, the system's generality, reliability and accuracy is demonstrated, and show that the well operability of this system can enable high-throughput detection of a small molecule in blood samples. The system can be further converted to rely on allosteric deoxyribozyme instead of allosteric ribozyme to recognize non-nucleic-acid targets and transduce the signal to CRISPR-Cas12a for amplification, likely making it easier for storage and more consistent in data generation as DNA possess a stability advantage over RNA. This (deoxy)ribozyme-assisted CRISPR-Cas12a system anticipates that it can facilitate bioanalysis in various scientific and clinical settings and further drive the development of clinical translation.

Making target sites in large structured RNAs accessible to RNA-cleaving DNAzymes through hybridization with synthetic DNA oligonucleotides

The 10-23 DNAzyme is one of the most active DNA-based enzymes, and in theory, can be designed to target any purine-pyrimidine junction within an RNA sequence for cleavage. However, purine-pyrimidine junctions within a large, structured RNA (lsRNA) molecule of biological origin are not always accessible to 10-23, negating its general utility as an RNA-cutting molecular scissor. Herein, we report a generalizable strategy that allows 10-23 to access any purine-pyrimidine junction within an lsRNA. Using three large SARS-CoV-2 mRNA sequences of 566, 584 and 831 nucleotides in length as model systems, we show that the use of antisense DNA oligonucleotides (ASOs) that target the upstream and downstream regions flanking the cleavage site can restore the activity (kobs) of previously poorly active 10-23 DNAzyme systems by up to 2000-fold. We corroborated these findings mechanistically using in-line probing to demonstrate that ASOs reduced 10-23 DNAzyme target site structure within the lsRNA substrates. This approach represents a simple, efficient, cost-effective, and generalizable way to improve the accessibility of 10-23 to a chosen target site within an lsRNA molecule, especially where direct access to the genomic RNA target is necessary.

DNAzyme and controllable cholesterol stacking DNA machine integrates dual-target recognition CTCs enable homogeneous liquid biopsy of breast cancer

Although circulating tumor cells (CTCs) have demonstrated considerable importance in liquid biopsy, their detection is limited by low concentrations and complex sample components. Herein, we developed a homogeneous, simple, and high-sensitivity strategy targeting breast cancer cells. This method was based on a non-immunological stepwise centrifugation preprocessing approach to isolate CTCs from whole blood. Precise quantification is achieved through the specific binding of aptamers to the overexpressed mucin 1 (MUC1) and human epidermal growth factor receptor 2 (HER2) proteins of breast cancer cells. Subsequently, DNAzyme cleavage and parallel catalytic hairpin assembly (CHA) reactions on the cholesterol-stacking DNA machine were initiated, which opened the hairpin structures T-Hg2+-T and C-Ag+-C, enabling multiple amplifications. This leads to the fluorescence signal reduction from Hg2+-specific carbon dots (CDs) and CdTe quantum dots (QDs) by released ions. This strategy demonstrated a detection performance with a limit of detection (LOD) of 3 cells/mL and a linear range of 5-100 cells/mL. 42 clinical samples have been validated, confirming their consistency with clinical imaging, pathology findings and the folate receptor (FR)-PCR kit results, exhibiting desirable specificity of 100% and sensitivity of 80.6%. These results highlight the promising applicability of our method for diagnosing and monitoring breast cancer.

Visualized lateral flow assay for logic determination of co-existing viral RNA fragments

Different types of pathogenic viruses that have common transmission path can be co-infected, inducing distinct disease procession in comparison to that infection of one. Also, in the post COVID-19 time, more types of respiratory infectious virus are becoming prevalent and are concurrent. Those bring an urgent need for detection of co-existing viruses. Here, we propose a visualized lateral flow assay for logic determination of co-existing viral RNA fragments. In the presence of specific viral RNA inputs, DNAzyme is de-blocked according to defined logic, and catalyzes the hydrolysis of hairpin-structural substrate. One of cleaved substrates contains DNAzyme domain to realize dual signal amplification, which obtains copious of the other cleaved substrates. The cleaved substrates act as linking strands for bridging DNA-modified gold nanoparticles onto lateral flow strip to induce coloration on test line. "AND", "OR" and "INHIBIT" controlled lateral flow assays are respectively demonstrated for co-existing viral RNA detection, and the visual results can be obtained by the same kind of prepared strip, without need of re-fabricating strips according to logic systems. The work provides a flexible, convenient, visual and logic-processing strategy for simultaneous analysis of co-existing viruses.

G-Quadruplex-Programmed Versatile Nanorobot Combined with Chemotherapy and Gene Therapy for Synergistic Targeted Therapy

Developing synergistic targeted therapeutics to improve treatment efficacy while reducing side effects has proven promising for anticancer therapies, but how to conveniently modulate multidrug cooperation remains a challenge. Here, a novel synergistic strategy using a G-quadruplex-programmed versatile nanorobot (G4VN) containing two subunits of DNAzyme (DzG4) and ligand-drug conjugates (LDCs) is proposed to precisely target tumors and then execute both gene silencing and chemotherapy. As the core module of this nanorobot, a well-designed G4 responding to a high level of K+ in tumor microenvironment smartly kills three birds with one stone, which makes two TfR aptamers proximate to improve their efficiency of targeting tumor cells, and in situ activates a split 10-23 DNAzyme to downregulate target mRNA expression, meanwhile promotes the cell uptake of a GSH-responsive LDCs to enhance drug efficacy. Such a design enables a potently synergistic anticancer therapy with low side effects in vivo, showing great promise for broad applications in precision disease treatment.

Recent advances in DNAzymes for bioimaging, biosensing and cancer therapy

DNAzymes, a class of single-stranded catalytic DNA with good stability, high catalytic activity, and easy synthesis, functionalization and modification properties, have garnered significant interest in the realm of biosensing and bioimaging. Their integration with fluorescent dyes or chemiluminescent moieties has led to remarkable bioimaging outcomes, while DNAzyme-based biosensors have demonstrated robust sensitivity and selectivity in detecting metal ions, nucleic acids, proteins, enzyme activities, exosomes, bacteria and microorganisms. In addition, by delivering DNAzymes into tumor cells, the mRNA therein can be cleaved to regulate the expression of corresponding proteins, which has further propelled the application of DNAzymes in cancer gene therapy and synergistic therapy. This paper reviews the strategies for screening attractive DNAzymes such as SELEX and high-throughput sequencing, and briefly describes the amplification strategies of DNAzymes, which mainly include catalytic hairpin assembly (CHA), DNA walker, hybridization chain reaction (HCR), DNA origami, CRISPR-Cas12a, rolling circle amplification (RCA), and aptamers. In addition, applications of DNAzymes in bioimaging, biosensing, and cancer therapy are also highlighted. Subsequently, the possible challenges of these DNAzymes in practical applications are further pointed out, and future research directions are suggested.

A novel viral RNA detection method based on the combined use of trans-acting ribozymes and HCR-FRET analyses

The diagnoses of retroviruses are essential for controlling the rapid spread of pandemics. However, the real-time Reverse Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR), which has been the gold standard for identifying viruses such as SARS-CoV-2 in the early stages of infection, is associated with high costs and logistical challenges. To innovate in viral RNA detection a novel molecular approach for detecting SARS-CoV-2 viral RNA, as a proof of concept, was developed. This method combines specific viral gene analysis, trans-acting ribozymes, and Fluorescence Resonance Energy Transfer (FRET)-based hybridization of fluorescent DNA hairpins. In this molecular mechanism, SARS-CoV-2 RNA is specifically recognized and cleaved by ribozymes, releasing an initiator fragment that triggers a hybridization chain reaction (HCR) with DNA hairpins containing fluorophores, leading to a FRET process. A consensus SARS-CoV-2 RNA target sequence was identified, and specific ribozymes were designed and transcribed in vitro to cleave the viral RNA into fragments. DNA hairpins labeled with Cy3/Cy5 fluorophores were then designed and synthesized for HCR-FRET assays targeting the RNA fragment sequences resulting from ribozyme cleavage. The results demonstrated that two of the three designed ribozymes effectively cleaved the target RNA within 10 minutes. Additionally, DNA hairpins labeled with Cy3/Cy5 pairs efficiently detected target RNA specifically and triggered detectable HCR-FRET reactions. This method is versatile and can be adapted for use with other viruses. Furthermore, the design and construction of a DIY photo-fluorometer prototype enabled us to explore the development of a simple and cost-effective point-of-care detection method based on digital image analysis.

Proximity-Dependent Activation of Split DNAzyme Kinase

Binary (also known as split) nucleic acid enzymes have emerged as novel tools in biosensors. We report a new split strategy to split the DNAzyme kinase into two independent and non-functional fragments, denoted Dk1sub and Dk1enz. In the presence of the specific target, their free ends are brought sufficiently close to interact with each other without the formation of Watson-Crick base pairings between Dk1sub and Dk1enz, thus allowing the DNA phosphorylation reaction. We term this approach proximity-dependent activation of split DNAzyme kinase (ProxSDK). The utility of ProxSDK is demonstrated by engineering a biosensing system that is capable of measuring specific DNA-protein interactions. We envision that the approach described herein will find useful applications in biosensing, imaging, and clinical diagnosis.

Design of a Membrane-Anchored DNAzyme-Based Molecular Machine for Enhanced Cancer Therapy by Customized Cascade Regulation

Synthetic DNAzyme-based structures enable dynamic cell regulation. However, engineering an effective and targeted DNAzyme-based structure to perform customizable multistep regulation remains largely unexplored. Herein, we designed a membrane-anchored DNAzyme-based molecular machine to implement dynamic inter- and intracellular cascade regulation, which realizes efficient T-cell/cancer cell interactions and subsequent receptor mediated cancer cell uptake. Using CD8+ T-cells and HeLa cancer cells as a proof of concept, we demonstrate that the designed DNAzyme-based molecular machine enables customized cascade regulation including (1) specific recognition between T-cells and cancer cells, (2) specific response and fluorescence sensing upon extracellular stimuli, and (3) cascade regulation including intercellular distance shortening, cell-cell communication, and intracellular delivery of anticancer drugs. Together, this work provides a promising pathway for customized cascade cell regulation based on a DNAzyme-based molecular machine, which enables enhanced cancer therapy by combining T-cell immunotherapy and chemotherapy.