Bioorthogonal Disassembly of Hierarchical DNAzyme Nanogel for High-Performance Intracellular microRNA Imaging

An in situ-boosted electrochemiluminescence biosensor for serotonin detection sensitized with Co3O4 nanoplates and self-feedback DNA recycling

Here, we described an in situ-boosted electrochemiluminescence (ECL) biosensor for serotonin detection sensitized with the catalysis of Co3O4 nanoplates and self-feedback DNA recycling (SFDR). Specifically, aptamer:S duplex was attached onto the surface of magnetic beads via amide bond. When serotonin presented, it competitively combined with aptamer from aptamer:S duplex. Then, the released S strands reacted with hairpin DNA (H) containing the silenced Mg2+-assisted DNAzyme site in the loop part that immobilized on CdS quantum dots (CdS QDs) modified electrode. The activating Mg2+-assisted DNAzyme cut off H and re-liberated S strands. Therefore, the Mg2+-DNAzyme-aided recycle happened to produce numerous residual single-stranded DNA segments and then reacted with Co3O4-modified P strands on the electrode surface. Such results directly introduced Co3O4 nanoplates close to CdS QDs, resulting in the reduction of H2O2 to •OH and the increase of ECL emission of CdS QDs in CdS QDs-H2O2 system. Based on such signal amplification strategy, a low detection limit of 1.5 pM was obtained for serotonin detection. This approach enabled the proposed ECL biosensor promising for the future application in the trace detection of serotonin.

Bifunctional MXene quantum dots-coated bimetallic Prussian blue analogues for sensitive sensing and accurate localization imaging of miRNAs in living cells

MicroRNAs (miRNAs) are involved in multiple cellular processes and play a critical role in clinical diagnosis. In-situ spatiotemporal imaging of miRNAs in living cells is tightly linked to the carcinogenesis and development of malignant tumors. Herein, we proposed a bifunctional nanosystem-based MXene quantum dots-coated bimetallic Prussian blue analogues (Co-Mn PBA@MQDs) to execute in-vitro sensing and intracellular imaging of miRNA in living cells. The 3D nanostructures of Co-Mn PBAs were regulated to slow down the coordination reaction rate by controlling the diffusion of metal clusters and ligand precursors, thereby anchoring MQDs as the carriers of DNA probes. The resulting Co-Mn PBA@MQDs nanoparticles with miRNA recognition ability exhibit excellent electrocatalytic and photoluminescence properties for target miRNA analysis. It reached miRNA detection limit of 0.37 fM (S/N = 3) with a wide linear range of 1 fM to 1 nM, and allowed distinguish family members without additional complex modifications. Meanwhile, DNA probe adsorbed on Co-Mn PBA@MQDs can provide delivery capacity for intracellular miRNA location, resulting in the in-situ monitoring and imaging of miRNA with deregulated expression levels in cancer cells. With these advantages, the developed strategy provides a paradigm for the rational design of the miRNA analysis system, which is expected to be widely applied to disease diagnosis and further theragnostic fields.

Programmed Fluorescence-Encoding DNA Nanoflowers for Cell-Specific-Target Multiplexed MicroRNA Imaging

The precise identification and differentiation of multiple microRNAs (miRNAs) with high spatial resolution in specific cells remain a significant challenge, primarily due to the limited availability of spectrally distinguishable fluorophores and the absence of cell-specific recognition capabilities. In this study, we introduce a programmed fluorescence-encoding DNA nanoflower (CNFs) system based on the self-assembly of rolling circle amplification (RCA), enabling multiplexed miRNA imaging in living cells. The CNFs system is rationally designed to consist of three key components: a CD63 aptamer region, dual fluorophore encoding regions, and an miRNA recognition region. The polyvalent tandem CD63 aptamer enhances the cellular targeting specificity and endocytic uptake efficiency. By controlling dual fluorophores and three levels of intensity within encoding regions, it generates 9 distinct barcodes for labeling multiple targets. Additionally, when conjugated with molecular beacons (MBs), CNFs facilitate the simultaneous detection of multiplexed intracellular miRNAs. Using this CNFs system, we successfully evaluated the expression profiles of nine miRNAs in breast cancer. Overall, we expect that this CNFs system will be a valuable tool for disease-related multiplex miRNAs biomarker imaging in specific cells and the exploration of miRNAs' molecular regulation mechanisms.

Imaging Low-Abundance, Short Cellular RNAs Using G-quadruplex FISH

Visualizing cellular RNAs enables spatial resolution at the single-cell level. Fluorescence in situ hybridization (FISH) is a facile tool; however, it is not sensitive enough to detect low-abundance or short RNAs in cells due to limited signal gain. Here, we present G-quadruplex FISH, a sensitive RNA imaging method that synergizes G-quadruplex peroxidase-driven tyramide deposition with proximity labeling chemistry. It eliminates nucleic acid amplification yet achieves efficient signal amplification through catalytic tyramide polymerization. Compared to conventional FISH, G-quadruplex FISH reduces background and enhances signal-to-background ratio, enabling the detection of RNAs down to 25.7 copies/cell. Its high-gain imaging enables the visualization of short RNAs in cells. Using G-quadruplex FISH, we explored the immunotoxicity of endotoxins and screened its antagonists. G-quadruplex FISH addresses FISH's sensitivity limitation, facilitating investigation of the roles of different RNAs involved in cellular function and disease.

Target-induced nanoparticle assemblies: a comprehensive review of strategies for nucleic acid functionalization, biosensing, and drug delivery applications

Fundamental studies on nanoparticle superstructures or core-satellite assemblies and their interactions with biomolecules have led to advancements in nanobiotechnology. Consequently, some novel nucleic acid (NA) biosensing, diagnostics, and imaging approaches have been developed by functionalizing the surface of nanoparticles with target-specific analytes. For functionalization, multivalent nanoparticles are chosen over monovalent ones because they can enhance the concentration of probes on the nanoparticle surface and simultaneously bind to multiple target sites, leading to specific and sensitive detection, primarily in the case of target NAs with low-abundance target. Selection of appropriate satellite (shell) and core nanoparticles is crucial for building assemblies that can improve the resistance of DNA against serum degradation and nuclease activity by several folds compared with those of un-assembled particles. Structural modification of NPs via covalent ligation with DNA or miRNA using synthetic click chemistry approaches resulted in the formation of dimers/tetramers, which could ease the delivery of DNA-intercalating drugs and simultaneously sense target biomarkers in the cellular environment, showing the synergistic applications of multivalent assemblies. This review provides an overview of the design strategies and chemistries involved in the loading of nucleic acid probes onto the NP surface, synthesis of PEG ligands, and purification and characterization techniques for assemblies (dimer, trimer, and multimer). In addition, the applications of NP assemblies in biosensing miRNA, strategies and challenges involved in the intracellular detection of miRNA, colorimetric, SERS, and electrochemical techniques for bacterial/virus detection, and drug delivery applications are discussed. Finally, the advantages, challenges, and future perspectives in commercializing this technology are comprehensively elucidated.

Construction of a Self-Assembled DNA Nanofirework for Signal Amplification and Intracellular miRNA Imaging

Nonenzymatic DNA catalytic amplification strategies have greatly improved the detection of biomolecules. However, the membrane barrier and the complex intracellular environment remain the two main challenges for efficient intracellular RNA imaging. Herein, we designed a self-assembled DNA nanofirework for amplified microRNA (miRNA) imaging in living cells. The self-assembled DNA nanofireworks exhibited high sensitivity and specificity for miRNA detection, achieving excellent internalization efficiency through endocytosis, while demonstrating enhanced biostability and biocompatibility. These properties enable powerful signal-amplified miRNA imaging in live cells. Under optimized conditions, this nanoprobe achieves a linear detection range of 0.5-8.0 nM for miRNA-21 with a detection limit of 89.3 pM. This design represents an optimal integration of DNA nanotechnology with nucleic acid amplification for intracellular biomolecule analysis, providing valuable insights for understanding the biological functions of important biomolecules in disease pathogenesis and potential therapeutic applications.

On-Demand Regulation of Catalytic DNA Circuits Using Phosphorylated Charge Reversal Peptides

Catalytic DNA circuits have emerged as a powerful tool for high-performance biosensing application; however, the establishment of a safe and efficient in vivo delivery system remains a critical bottleneck. Peptides serve as attractive carriers due to their rich chemical diversity, excellent biocompatibility, high loading capacity, and specific binding ability, making them ideal candidates for the on-demand regulation of DNA circuits-yet remains largely unexplored. In this study, we developed a multifunctional enzyme-responsive peptide (ERP) for the efficient loading and specific intracellular delivery and release of catalytic circuitry probes through a phosphorylation-based charge reversal procedure. This ERP-programmed catalytic DNA circuit enables the precise, spatially controllable in vivo imaging of microRNA (miRNA). The multifunctional cationic peptide formed a stable nanocomplex with anionic DNA cargo via strong electrostatic interactions, thus protecting the DNA probes from degradation in biological environments. Moreover, with the ability to actively targeting tumor cells and facilitate endogenous phosphorylation-guided release of DNA probes, this multifunctional peptide could significantly reduce the nonspecific delivery of probes to healthy tissues, thereby minimizing unwanted off-site signal leakage. By the integration of cell-selective delivery and site-specific stimulation, this endogenously regulated and multiply guaranteed DNA circuit system paves a simple yet effective way for disease diagnosis.

Redox-stimulated catalytic DNA circuit for high-fidelity imaging of microRNA and in situ interpretation of the relevant regulatory pathway

Biomolecules play essential roles in regulating the orderly progression of biochemical reaction networks. DNA-based biocircuits supplement an attractive and ideal approach for the visual imaging of endogenous biomolecules, yet their sensing performance is commonly encumbered by the undesired signal leakage. To solve this issue, here we proposed a glutathione (GSH)-activated DNA circuit for achieving the spatio-selective microRNA imaging through the successive response of a GSH-specific activation procedure and a non-enzymatic catalytic signal amplification procedure. In this design, by incorporating a disulfide bond into the pre-sealed nucleic acid probe, the uncontrolled circuitry leakage could be effectively ameliorated. In target cancer cells with high-abundant GSH and miR-21, endogenous GSH recognized and cleaved the pre-installed disulfide bond within DNA probes, thereby restoring the activity of circuitry components. The miR-21 then catalyzed the specific operation of circuitry for generating an amplified readout signal. We demonstrate that this system not only enables the effective discriminations of various cell types, but also contributes to the exploration of the correlationship between GSH and miR-21. This on-site activated DNA circuit can be extended to the robust analysis and exploration of different biomolecular interactions, offering a reliable reference for the in-depth understanding of biochemical interaction networks.

A photo-elutable 8-17 DNAzyme labeling and PCR-free colorimetric quantification strategy for 5-hydroxymethylcytosine in mammalian genomic DNA

We developed a PCR-free, cost-effective colorimetric assay using gold nanoparticles (AuNPs) to quantify 5-hydroxymethylcytosine (5hmC) without expensive MS instruments or antibodies. This method employs a photo-elutable 8-17 DNAzyme label specific to 5hmC sites, achieving accuracy comparable to ELISA when measuring 5hmC levels in various ICR mouse tissues.

Engineering DNA Nanodevices with Multi-site Recognition and Multi-signal Output for Accurate Intracellular LncRNA Imaging

Dynamic DNA nanodevices, known for their high programmability and controllability, are pivotal in intracellular biomarker imaging. However, these nanodevices often suffer from inadequate detection sensitivity and specificity due to limited cellular loading capacity and low signal feedback. Herein, we engineered an integrated multi-site recognition and multi-signal output of four-leaf clover dynamic DNA nanodevice (MEMORY) that enables sensitive and accurate intracellular long noncoding RNA (lncRNA) imaging. MEMORY features one fluorophore (FAM)-modified cross-shaped structure as spatial-confinement scaffolds loaded with four identical quenchers (BHQ1)-modified recognition probes (RPs), ensuring a low background signal initially. In the presence of target lncRNA, the multiple recognition sites of MEMORY facilitate hybridization with the target to selectively release the RPs, exposing the toehold region and outputting the green fluorescence (FAM) signal. Furthermore, the exposed toehold region can trigger efficient and rapid hybridization chain reaction (HCR) amplification, outputting the red fluorescence (Cy5) signal. MEMORY's multiple recognition sites increase the likelihood of target collisions, enhancing reaction efficiency, while its multi-signal output provides sequential feedback through FAM and Cy5, boosting overall signal intensity. With the lncRNA metastasis-related lung adenocarcinoma transcript 1 (MALAT1) as a detection model, MEMORY offers a linear detection range from 1 pM to 100 nM, with a limit of detection of 0.29 pM. We demonstrated that MEMORY can differentiate between normal and tumor cells based on intracellular MALAT1 imaging. This integrated DNA nanodevice will offer valuable tools for sensitive and accurate imaging of intracellular biomarkers.

Self-Adaptive Activation of DNAzyme Nanoassembly for Synergistically Combined Gene Therapy

DNAzyme represents a promising gene silencing toolbox yet is obstructed by the poor substrate accessibility in specific cells. Herein, a compact DNA nanoassembly, incorporating multimeric therapeutic DNAzyme, was prepared for selective delivery of gene-silencing DNAzyme with requisite cofactors and auxiliary chemo-drugs. By virtue of the sequence-conservative duplex-specific nuclease, the endogenous miRNA catalyzes the successive and site-specific cleavage of DNA nanoassembly substrate (nominated as the localized RNA walking machine) and thus ensures the liberation/activation of therapeutic agents with high accuracy and efficacy. The miR-10b-stimulated DNAzyme was designed to downregulate the TWIST transcription factor, an upstream promotor of miR-10b, thus acquiring the self-sufficient downregulation of TWIST/miR-10b signaling nodes (self-adaptive negative feedback loop) for abrogating tumor metastasis and chemo-resistance issues.

Biosensor development for diabetes diagnosis: Determining relevant miRNA using a newly developed N-annulated perylene fluorescent dye

MicroRNAs (miRNAs) have emerged as essential biomarkers for disease diagnosis, and several techniques are available to determine type 2 diabetes (T2D) relevant miRNAs. However, detecting circulating miRNAs can be challenging due to their small size, low abundance, and high sequence similarity, often requiring sensitive detection approaches combined with additional amplification processes. Laser-induced fluorescence (LIF) is a classic analytical method suitable for sensitively detecting trace amounts of nucleotide acid. Duplex-specific nuclease (DSN)-mediated amplification recently gained attention due to its catalytic activity based on target recycling, demonstrating a promising approach for miRNA amplification. This work developed a novel N-annulated perylene fluorescent dye to create a biosensor to analyze the miRNA (miR-223) relevant to T2D. The amine-reactive fluorescent dye assists the amidation reaction for nucleotide labeling, giving the oligonucleotide probe a high fluorescence quantum yield and sufficient water solubility. By combining the locked nucleic acid (LNA) modified oligonucleotide fluorescent probe to enhance the stability of LNA/RNA hybrids, thereby improving the DSN-mediated target miR-223 recycling for signal amplification, the proposed biosensor can highly selectively determine miR-223 with a limit of detection (LOD, S/N = 3) of 9.5 pM. When applied to real-world samples, the biosensor demonstrated its potential to distinguish between T2D patients and healthy controls.

Harnessing Demethylase-Regulated Catalytic DNA Circuit for In-Situ Investigation of the Regulatory Connection with MicroRNA

Insight into the epigenetic modulation-correlated molecule interactions has significant implications for the in-depth understanding of intracellular intricate biological networks. However, there is currently a lack of reliable biological tools for elucidating the potential correlation between epigenetic regulators and relevant genes, e.g., microRNAs (miRNAs). Herein, an alkB homologue 5 (ALKBH5, a key epigenetic regulator)-modulated catalytic DNA circuit (ACD) was constructed by grafting a N6-methyladenosine (m6A)-caged I-R3 DNAzyme into the circuitry components for achieving the on-site miRNA imaging in living cells. Specifically, the catalytic activity of I-R3 DNAzyme could be effectively suppressed by the m6A modification situated at its highly sequence-conserved core region and then be selectively restored through the ALKBH5-mediated demethylation pathway. And the ALKBH5-activated I-R3 DNAzyme allowed the highly efficient DNA cleaving reaction in the presence of DNAzyme cofactors, resulting in the liberation of catalytic hairpin assembly (CHA) reactants. Subsequently, target miRNA triggered the CHA circuit to produce a duplex DNA product while releasing the miRNA analyte. The liberated miRNA could autonomously trigger the next round of the CHA assembly cycle for generating the amplified fluorescence readout. By virtue of the stimuli-responsive activation and the CHA amplification circuit, the ACD system achieved highly specific and sensitive imaging of miRNA in tumor cells. Moreover, this efficiently and reliably ALKBH5-activated DNA circuit is demonstrated to reveal the underlying relationship between activator ALKBH5 and miRNA. Overall, the developed ACD system provides a promising tool for the robust on-site profiling of epigenetic-involved signal pathways, thus displaying great potential in bioanalytical applications.

DNA Hydrogels for Cancer Diagnosis and Therapy

Nucleic acids, because of their precise pairing and simple composition, have emerged as excellent materials for the formation of gels. The application of DNA hydrogels in the diagnosis and therapy of cancer has expanded significantly through research on the properties and functions of nucleic acids. Functional nucleic acids (FNAs) such as aptamers, Small interfering RNA (siRNA), and DNAzymes have been incorporated into DNA hydrogels to enhance their diagnostic and therapeutic capabilities. This review discusses various methods for forming DNA hydrogels, with a focus on pure DNA hydrogels. We then explore the innovative applications of DNA hydrogels in cancer diagnosis and therapy. DNA hydrogels have become essential biomedical materials, and this review provides an overview of current research findings and the status of DNA hydrogels in the diagnosis and therapy of cancer, while also exploring future research directions.

A Multifunctional DNA Nanoassembly for Cancer Cell Detection and Combined Gene-Chemotherapy Therapy

Although DNAzyme is a promising gene therapy agent, low cellular uptake efficiency, poor biological stability, and the unsatisfactory effect of monotherapy limit its development. Herein, a multifunctional DNA nanoassembly (RCA product-aptamer-DNAzyme, RAD) was constructed for cancer cell detection and targeted delivery of doxorubicin (DOX) and DNAzyme. Briefly, the rolling circle amplification (RCA) product was employed as a scaffold, and each repeated sequence was designed to combine with three single-stranded DNA (ssDNA), which carried the aptamer AS1411 sequence, fluorescent group, and DNAzyme sequence, respectively. Up to 40 groups of ssDNA can be assembled into an RCA product, resulting in a high affinity for cancer cells and stronger fluorescent signals. Due to the high binding affinity, RAD displayed high sensitivity for the detection of HepG-2 cells (the limit of detection was 200 cells/mL). In addition, with the formation of the double helix structure, each RAD could load up to 200 DOX molecules. Subsequently, RAD could efficiently and selectively deliver DOX and DNAzyme into cancer cells through the multivalent interaction between the aptamers and membrane nucleolin. Then, the released DNAzyme could recognize and cleave survivin mRNA under the action of Mg2+, leading to the apoptosis of HepG-2 cells for gene therapy, while DOX inserted into intracellular DNA to inhibit cell proliferation, realizing chemotherapy. According to the results, RAD-DOX displayed enhanced therapeutic effects compared with individual gene therapy or chemotherapy, and RAD could protect membrane nucleolin-negative cells from the effects of DOX. Overall, given the enhanced serum stability, high drug-loading capacity, and excellent selective cellular uptake ability of RAD, this strategy shows great potential in the field of cancer therapy.

On-Site Multiply Stimulated Self-Confinement of an Integrated DNA Cascade Circuit for Highly Reliable Intracellular Imaging of miRNA and In Situ Interrogation of the Relevant Regulatory Pathway

Artificial DNA circuits represent a versatile yet promising toolbox for in situ monitoring and concomitant regulation of diverse biological events within live cells. Nonetheless, their performance is significantly impeded by the diffusion-dominated slow reaction kinetics and the uncontrollable off-target activation. Herein, a self-localized cascade (SLC) circuit is reported for the robust and efficient microRNA (miRNA) analysis in living cells. The SLC circuit consists of the cell-specific localization module and the analyte-specific signal amplification module. By integrating the reaction probes of these two modules, the complexity of the system is reduced to realize the responsive co-localization of circuitry probes and the simultaneous cascade signal amplification. Taking advantage of the specifically activated, self-localized, and cascade design, the SLC circuit successfully achieves the robust miRNA-21 (miR-21) imaging and the accurate cells differentiation. Moreover, the reverse regulation mechanism is successfully explored between messenger RNA (mRNA) and miRNA through the engineered SLC circuit and further elucidates the underlying signaling pathways between them. Therefore, the SLC circuit provides a powerful tool for the sensitive detection of intracellular biomolecules and the study of the corresponding cell regulatory mechanisms.

The Acid-Stimulated Self-Assembled DNA Nanonetwork for Sensitive Detection and Living Cancer Cell Imaging of MicroRNA-221

Herein, a novel functional DNA structure, acid-stimulated self-assembly DNA nanonetwork (ASDN), was proposed for miRNA-221 sensitive detection and high-resolution living cancer cell imaging. Significantly, the self-assembly of ASDN only occurred in the acidic extracellular environment of cancer cells, which could be endocytosed by cancer cells to eliminate the interference of noncancer cells and deliver the ASDN into cancer cells. Subsequently, endogenous miRNA-221 could trigger the catalytic hairpin assembly within ASDN, resulting in the separation of the fluorophore Cy5 and the quencher BHQ2 to recover the substantial Cy5 fluorescence signals, thus achieving signal amplification for sensitive detection of miRNA-221 with a detection limit of 5.5 pM, as well as facilitating high-resolution and low-background imaging of miRNA-221 in cancer cells. In consequence, this strategy provides an innovative DNA nanonetwork to distinguish cancer cells from other cells for sensitive detection of biomarkers, offering a meaningful reference for the application of DNA nanostructure self-assembly technology in relevant fundamental research and disease diagnosis.

Light-Triggered Plasmonic DNAzyme Walker Enables Precise Subcellular Molecular Imaging with Reduced Off-Mitochondria Signal Leakage

The development of highly sensitive and precise imaging techniques capable of visualizing crucial molecules at the subcellular level is essential for elucidating mitochondrial functions and uncovering novel mechanisms in biological processes. However, traditional molecular imaging strategies are still limited by off-mitochondria signal leakage because of the "always-active" sensing mode. To address this limitation, we have developed a light-triggered activation sequence activated plasmonic DNAzyme walker (PDW) for accurate subcellular molecular imaging by the combination of an organelle localized strategy, upconversion nanotechnology, and a plasmon enhanced fluorescence (PEF) technique. Exploiting the advantage of light activation enables precise control over when and where to activate the probe's sensing function, effectively reducing off-mitochondria signal leakage as validated by the dynamic monitoring of changes in off-mitochondria signals during the mitochondrial entry process. Furthermore, by leveraging the PEF capability of triangular gold nanoprisms (Au NPRs), the fluorescence intensity can be enhanced by approximately 11.9 times, ensuring highly sensitive and accurate subcellular molecular imaging.

On-Site Visualization Assay for Tumor-Associated miRNAs: Using Ru@TiO2 as a Peroxidase-like Nanozyme

Accurate diagnosis of highly aggressive and deadly tumors is essential for effective treatment and improved patient outcomes, and microRNAs (miRNAs) have emerged as crucial biomarkers for their roles in tumor initiation, progression, and metastasis. Herein, we present an on-site visualization colorimetric assay for tumor-associated miRNAs using ruthenium nanoparticle decorated titanium dioxide nanoribbon (Ru@TiO2) as a peroxidase-like (POD) nanozyme. Remarkably, the Ru@TiO2 nanozyme can catalyze the oxidation of chromogenic substrates through its POD-like activity, which is effectively inhibited by pyrophosphate generated during the rolling circle amplification process, thereby enabling miRNA detection through a visible colorimetric readout. This approach provides a highly sensitive and specificity assay for miRNAs in diluted human serum with a detection limit of 100 pM. It shows great potential for clinical diagnostics and biological research, offering a promising tool for early cancer diagnosis and molecular diagnostics.

A splice-switch oligonucleotide loaded self-cleavable DNA nanogel

A self-cleavable DNA nanogel loaded with splice-switch oligonucleotide (SSO) has been developed. Under acidic conditions (pH 5.0), cleavage of the acid-labile chemical linker and generation of the i-motif structure led to the disintegration of the DNA nanogel and efficient release of SSO in its unaltered native state.

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 Methyl-Engineered DNAzyme for Endogenous Alkyltransferase Monitoring and Self-Sufficient Gene Regulation

The on-demand gene regulation is crucial for extensively exploring specific gene functions and developing personalized gene therapeutics, which shows great promise in precision medicines. Although some nucleic acid-based gene regulatory tools (antisense oligonucleotides and small interfering RNAs) are devised for achieving on-demand activation, the introduction of chemical modifications may cause undesired side effects, thereby impairing the gene regulatory efficacy. Herein, a methyl-engineered DNAzyme (MeDz) is developed for the visualization of endogenous alkyltransferase (AGT) and the simultaneous self-sufficiently on-demand gene regulation. The catalytic activity of DNAzyme can be efficiently blocked by O6-methylguanine (O6MeG) modification and specifically restored via the AGT-mediated DNA-repairing pathway. This simply designed MeDz is demonstrated to reveal AGT of varying expression levels in different cells, opening the possibility to explore the AGT-related biological processes. Moreover, the AGT-guided MeDz exhibits cell-selective regulation on the human early growth response-1 (EGR-1) gene, with efficient gene repression in breast cancer cells and low effectiveness in normal cells. The proposed MeDz offers an attractive strategy for on-demand gene regulation, displaying great potential in biomedical applications.

Responsive DNA hydrogels: design strategies and prospects for biosensing

Hydrogels, water-filled networks that can adapt to external stimuli by altering their volume, are known for their high flexibility and biocompatibility. DNA, a critical biomolecule renowned for its exceptional characteristics including information transmission, molecular recognition, and editability, has found widespread applications in the biosensing field as well. The integration of these two biomaterials offers promising opportunities for the development of novel biosensors with enhanced sensitivity, specificity, and adaptability. Therefore, by virtue of the collective features, researchers have recently focused on the construction of responsive DNA hydrogel systems. This feature article describes recent developments in fabricating DNA hydrogels and their applications in the biosensing area. Initially, it focuses on the design strategies employed in preparing DNA hydrogels, encompassing both pure DNA hydrogels and hybridized DNA hydrogels. Subsequently, it summarizes the use of DNA hydrogels in biosensing applications, highlighting their applications in visual detection, electrochemical sensing, and optical biosensing analyses. Furthermore, the underlying responsive mechanisms within these biosensing systems are also described. Lastly, this article presents a comprehensive discussion on the existing challenges and prospects of responsive DNA hydrogels, offering insights into their potential to revolutionize the field of biosensing.

Endogenous Glutathione-Activated Nucleic Acid Molecular Circuitry for Cell-Specific MicroRNA Imaging

Sensitive and reliable microRNA imaging in living cells has significant implications for clinical diagnosis and monitoring. Catalytic DNA circuits have emerged as potent tools for tracking these intracellular biomarkers and probing the corresponding biochemical processes. However, their utility is hindered by the low resistance to external interference, leading to undesired off-site activation and consequent signal leakage. Therefore, achieving the endogenous control of the DNA circuit's activation is preferable to the reliable target analysis in living cells. In this study, we attempted to address this challenge by engineering a simple yet effective endogenous glutathione (GSH)-regulated hybridization chain reaction (HCR) circuit for acquiring high-contrast miRNA imaging. Initially, the HCR hairpin reactants were blocked by the engineered disulfide-integrated DNA duplex, thus effectively passivating their sensing function. And the precaged HCR hairpin was liberated by the cell-specific GSH molecule, thus initiating the HCR system for selectively amplified detection of microRNA-21 (miR-21). This approach prevented unwanted signal leakage before exposure into target cells, thus ensuring robust miR-21 imaging with high accuracy and reliability in specific tumor cells. Moreover, the endogenously responsive HCR circuit established a link between the small regulatory factors and miRNA, thereby enhancing the signal gain. In summary, the endogenously activatable DNA circuit represents a versatile toolbox for robust bioanalysis and exploration of potential signaling pathways in living cells.

Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications

Nucleic acids exhibit exceptional functionalities for both molecular recognition and catalysis, along with the capability of predictable assembly through strand displacement reactions. The inherent programmability and addressability of DNA probes enable their precise, on-demand assembly and accurate execution of hybridization, significantly enhancing target detection capabilities. Decades of research in DNA nanotechnology have led to advances in the structural design of functional DNA probes, resulting in increasingly sensitive and robust DNA sensors. Moreover, increasing attention has been devoted to enhancing the accuracy and sensitivity of DNA-based biosensors by integrating multiple sensing procedures. In this review, we summarize various strategies aimed at enhancing the accuracy of DNA sensors. These strategies involve multiple guarantee procedures, utilizing dual signal output mechanisms, and implementing sequential regulation methods. Our goal is to provide new insights into the development of more accurate DNA sensors, ultimately facilitating their widespread application in clinical diagnostics and assessment.

Detecting mir-155-3p through a Molecular Beacon Bead-Based Assay

Lung cancer (LC) is recognized as one of the most prevalent and lethal cancers worldwide, underscoring an urgent need for innovative diagnostic and therapeutic approaches. MicroRNAs (miRNAs) have emerged as promising biomarkers for several diseases and their progression, such as LC. However, traditional methods for detecting and quantifying miRNAs, such as PCR, are time-consuming and expensive. Herein, we used a molecular beacon (MB) bead-based assay immobilized in a microfluidic device to detect miR-155-3p, which is frequently overexpressed in LC. The assay relies on the fluorescence enhancement of the MB upon binding to the target miRNA via Watson and Crick complementarity, resulting in a conformational change from a stem-loop to a linear structure, thereby bringing apart the fluorophores at each end. This assay was performed on a microfluidic platform enabling rapid and straightforward target detection. We successfully detected miR-155-3p in a saline solution, obtaining a limit of detection (LOD) of 42 nM. Furthermore, we evaluated the method's performance in more complex biological samples, including A549 cells' total RNA and peripheral blood mononuclear cells (PBMCs) spiked with the target miRNA. We achieved satisfactory recovery rates, especially in A549 cells' total RNA.

Engineering of a DNAzyme-Based dimeric G-quadruplex rolling circle amplification for robust analysis of lead ion

Detecting heavy metal pollution, particularly lead ion (Pb2⁺) contamination, is imperative for safeguarding public health. In this study, we introduced an innovative approach by integrating DNAzyme with rolling circle amplification (RCA) to propose an amplification sensing method termed DNAzyme-based dimeric-G-quadruplex (dimer-G4) RCA. This sensing approach allows for precise and high-fidelity Pb2⁺ detection. Strategically, in the presence of Pb2⁺, the DNAzyme undergoes substrate strand (S-DNA) cleavage, liberating its enzyme strand (E-DNA) to prime isothermal amplification. This initiates the RCA process, producing numerous dimer-G-Quadruplexes (dimer-G4) as the signal reporting transducers. Compared to conventional strategies using monomeric G-quadruplex (mono-G4) as the reporting transducers, these dimer-G4 structures exhibit significantly enhanced fluorescence when bound with Thioflavin T (ThT), offering superior target signaling ability for even detection of Pb2⁺ at low concentration. Conversely, in the absence of Pb2⁺, the DNAzyme structure remains intact so that no primers can be produced to cause the RCA initiation. This nucleic acid amplification-based Pb2⁺ detection method combing with the high specificity of DNAzymes for Pb2⁺ recognition ensures highly sensitive detection of Pb2+ with a detection limit of 0.058 nM, providing a robust tool for food safety analysis and environmental monitoring.

A Methylation-Gated DNAzyme Circuit for Spatially Controlled Imaging of MicroRNA in Cells and Animals

Epigenetic modification plays an indispensable role in regulating routine molecular signaling pathways, yet it is rarely used to modulate molecular self-assembly networks. Herein, we constructed a bioorthogonal demethylase-stimulated DNA circuitry (DSC) system for high-fidelity imaging of microRNA (miRNA) in live cells and mice by eliminating undesired off-site signal leakage. The simple and robust DSC system is composed of a primary cell-specific circuitry regulation (CR) module and an ultimate signal-transducing amplifier (SA) module. After the modularly designed DSC system was delivered into target live cells, the DNAzyme of the CR module was site-specifically activated by endogenous demethylase to produce fuel strands for the subsequent miRNA-targeting SA module. Through the on-site and multiply guaranteed molecular recognitions, the lucid yet efficient DSC system realized the reliably amplified in vivo miRNA sensing and enabled the in-depth exploration of the demethylase-involved signal pathway with miRNA in live cells. Our bioorthogonally on-site-activated DSC system represents a universal and versatile biomolecular sensing platform via various demethylase regulations and shows more prospects for more different personalized theragnostics.

Dark-field imaging and fluorescence dual-mode detection of microRNA-21 in living cells by core-satellite plasmonic nanoprobes

The in situ precise quantification and simultaneous imaging of low abundance microRNAs (miRNAs) within living cells is critical for cancer diagnosis, yet it remains a significant challenge. Leveraging the excellent sensitivity and spatiotemporal resolution of dark-field microscopy (DFM) and fluorescence imaging, we have successfully devised a novel detection approach using dual-signal reporter probes (DSRPs). These probes allow for highly sensitive detection of miRNA-21 in living cells via toehold-mediated strand displacement cascades. The DSRPs were constructed by Au nanoparticles and Ag nanoclusters core-satellite nanostructures. After the recognition of miRNA-21, the strand displacement cascades were triggered, inducing the disassembly of the Au/Ag core-satellite nanostructure with apparent scattering intensity decrease and peak wavelength shifts. Additionally, the fluorescence of Ag clusters could be recovered and further enhanced when in close proximity to specific guanine-rich strands. The dual-signal response capability enables the accurate detection of miRNA-21 from 1 fM to 1 nM, with a limit of detection reached 0.75 fM. DFM and fluorescent imaging of living cells efficiently confirms the applicable detection of miRNA-21 in complex detection media. The biosensor based on DSRPs represents a promising nanoplatform for visual monitoring and imaging of biomolecules in living cells, even at the single particle level.

Recent advances in functional nucleic acid decorated nanomaterials for cancer imaging and therapy

Nanomaterials possess unusual physicochemical properties including unique optical, magnetic, electronic properties, and large surface-to-volume ratio. However, nanomaterials face some challenges when they were applied in the field of biomedicine. For example, some nanomaterials suffer from the limitations such as poor selectivity and biocompatibility, low stability, and solubility. To address the above-mentioned obstacles, functional nucleic acid has been widely served as a powerful and versatile ligand for modifying nanomaterials because of their unique characteristics, such as ease of modification, excellent biocompatibility, high stability, predictable intermolecular interaction and recognition ability. The functionally integrating functional nucleic acid with nanomaterials has produced various kinds of nanocomposites and recent advances in applications of functional nucleic acid decorated nanomaterials for cancer imaging and therapy were summarized in this review. Further, we offer an insight into the future challenges and perspectives of functional nucleic acid decorated nanomaterials.

Multiply Guaranteed Catalytic DNA Circuit for Cancer-Cell-Selective Imaging of miRNA and Robust Evaluation of Drug Resistance

Catalytic DNA circuits are desirable for sensitive bioimaging in living cells; yet, it remains a challenge to monitor these intricate signal communications because of the uncontrolled circuitry leakage and insufficient cell selectivity. Herein, a simple yet powerful DNA-repairing enzyme (APE1) activation strategy is introduced to achieve the site-specific exposure of a catalytic DNA circuit for realizing the selectively amplified imaging of intracellular microRNA and robust evaluation of the APE1-involved drug resistance. Specifically, the circuitry reactants are firmly blocked by the enzyme recognition/cleavage site to prevent undesirable off-site circuitry leakage. The caged DNA circuit has no target-sensing activity until its circuitry components are activated via the enzyme-mediated structural reconstitution and finally transduces the amplified fluorescence signal within the miRNA stimulation. The designed DNA circuit demonstrates an enhanced signal-to-background ratio of miRNA assay as compared with the conventional DNA circuit and enables the cancer-cell-selective imaging of miRNA. In addition, it shows robust sensing performance in visualizing the APE1-mediated chemoresistance in living cells, which is anticipated to achieve in-depth clinical diagnosis and chemotherapy research.

Renewable Electrochemiluminescence Biosensor Based on Eu-MOGs as a Highly Efficient Emitter and a DNAzyme-Mediated Dual-drive DNA Walker as a Signal Amplifier for Ultrasensitive Detection of miRNA-222

Herein, novel europium metal-organic gels (Eu-MOGs) with excellent cathode electrochemiluminescence (ECL) emission are first used to construct biosensors for the ultrasensitive detection of miRNA-222. Impressively, N and O elements of organic ligand 2,2':6,2″-terpyridine 4,4',4″-tricarboxylic acid (H3-tctpy) can perfectly coordinate with Eu3+ to form Eu-MOGs, which not only reduce nonradiative transition caused by the intramolecular free rotation of phenyl rings in other MOGs to enhance the ECL signal with extraordinary ECL efficiency as high as 37.2% (vs the [Ru(bpy)3]2+/S2O82- ECL system) but also reinforce ligand-to-metal charge transfer (LMCT) by the strong affinity between Eu3+ and N and O elements to greatly improve the stability of ECL signals. Besides, an improved nucleic acid cascade amplification reaction is developed to greatly raise the conversion efficiency from target miRNA-222 to a DNAzyme-mediated dual-drive DNA walker as output DNA, which can simultaneously shear the specific recognition sites from two directions. In that way, the proposed biosensor can further enhance the detection sensitivity of miRNA-222 with a linear range of 10 aM-1 nM and a detection limit (LOD) of 8.5 aM, which can also achieve an accurate response in cancer cell lysates of MHCC-97L and HeLa. Additionally, the biosensor can be self-regenerated by the folding/unfolding of related triplets with pH changes to simplify experimental operations and reduce the cost. Hence, this work proposed novel MOGs with stable and intense ECL signals for the construction of a renewable ECL biosensor, supplying a reliable detection method in biomarker analysis and disease diagnosis.

Programming the Assembly of Oligo-Adenine with Coralyne into a pH-Responsive DNA Hydrogel

External stimuli-responsive DNA hydrogels present interesting platforms for drug loading and triggered release. Typically, drug molecules are encapsulated within three-dimensionally hybridized DNA networks. However, the utilization of drug molecules as cofactors to facilitate the directed assembly of DNA strands into hydrogel frameworks and their subsequent controlled release remains to be explored. Herein, we introduce the guided assembly of oligo-adenine (A-strand) into an acidic pH-responsive DNA hydrogel using an anticancer drug, coralyne (COR), as a low-molecular-weight cofactor. At pH 7, COR orchestrates the assembly of A-strand into an antiparallel duplex configuration cross-linked by A-COR-A units at a stoichiometric ratio of one COR cofactor per four adenine bases, resulting in a DNA hydrogel characterized by A-COR-A duplex bridges. At pH 4-5, the instability of A-COR-A units results in the disintegration of the duplex into its constituent components, leading to the release of COR and simultaneous dissociation of the DNA hydrogel matrix. This study introduces a method by which drug molecules, exemplified here by COR, facilitate the direct formation of a supramolecular cofactor-DNA complex, subsequently leading to the creation of a stimuli-responsive DNA hydrogel. This approach may inspire future investigations into DNA hydrogels tailored for controlled drug encapsulation and release applications.

Photoactivatable Engineering of CRISPR/Cas9-Inducible DNAzyme Probe for In Situ Imaging of Nuclear Zinc Ions

DNAzyme-based fluorescent probes for imaging metal ions in living cells have received much attention recently. However, employing in situ metal ions imaging within subcellular organelles, such as nucleus, remains a significant challenge. We developed a three-stranded DNAzyme probe (TSDP) that contained a 20-base-pair (20-bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure. With this design, the CRISPR/Cas9-inducible imaging of nuclear Zn2+ is demonstrated in living cells. Moreover, the superiority of CRISPR-DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn2+ in both HeLa cells and mice. Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal-associated biology.

Orthogonally Sequential Activation of Self-Powered DNAzymes Cascade for Reliable Monitoring of mRNA in Living Cells

Ratiometric imaging of tumor-related mRNA is significant, yet spatiotemporally resolved regulation on the ratiometric signals to avoid non-specific activation in the living cells remains challenging. Herein, orthogonally sequential activation of concatenated DNAzyme circuits is, first, developed for Spatio Temporally regulated Amplified and Ratiometric (STAR) imaging of TK1 mRNA inside living cells with enhanced reliability and accuracy. By virtue of the synthesized CuO/MnO2 nanosheets, orthogonally regulated self-powered DNAzyme circuits are operated precisely in living cells, sequentially activating two-layered DNAzyme cleavage reactions to achieve the two ratiometric signal readouts successively for reliable monitoring of low-abundance mRNA in living cells. It is found that the ratiometric signals can only be derived from mRNA over-expressed tumor cells, also irrespective of probes' delivery concentration. The presented approach could provide new insight into orthogonally regulated ratiometric systems for reliable imaging of specific biomarkers in living cells, benefiting disease precision diagnostics.

Multienzymatic disintegration of DNA-scaffolded magnetic nanoparticle assembly for malarial mitochondrial DNA detection

Early diagnosis of malaria can prevent the spread of disease and save lives, which, however, remains challenging in remote and less developed regions. Here we report a portable and low-cost optomagnetic biosensor for rapid amplification and detection of malarial mitochondrial DNA. Bioresponsive magnetic nanoparticle assemblies are constructed by using nucleic acid scaffolds containing endonucleolytic DNAzymes and their substrates, which can be activated by the presence of target DNA and self-disintegrated to release magnetic nanoparticles for optomagnetic quantification. Specifically, target molecules can induce padlock probe ligation and subsequent one-pot homogeneous cascade reactions consisting of nicking-enhanced rolling circle amplification, DNAzyme-assisted nucleic acid recycling, and strand-displacement-driven disintegration of the magnetic assembly. With an optimized magnetic actuation process for reaction acceleration, a detection limit of 1 fM can be achieved by the proposed biosensor with a total assay time of ca. 90 min and a dynamic detection range spanning 3 orders of magnitude. The robustness of the system was validated by testing target molecules spiked in 5% serum samples. Clinical sample validation was conducted by testing malaria-positive clinical blood specimens, obtaining quantitative results concordant with qPCR measurements.

Simulation-Assisted DNA Nanodevice Serve as a General Optical Platform for Multiplexed Analysis of Micrornas

Small frame nucleic acids (FNAs) serve as excellent carrier materials for various functional nucleic acid molecules, showcasing extensive potential applications in biomedicine development. The carrier module and function module combination is crucial for probe design, where an improper combination can significantly impede the functionality of sensing platforms. This study explores the effect of various combinations on the sensing performance of nanodevices through simulations and experimental approaches. Variances in response velocities, sensitivities, and cell uptake efficiencies across different structures are observed. Factors such as the number of functional molecules loaded, loading positions, and intermodular distances affect the rigidity and stability of the nanostructure. The findings reveal that the structures with full loads and moderate distances between modules have the lowest potential energy. Based on these insights, a multisignal detection platform that offers optimal sensitivity and response speed is developed. This research offers valuable insights for designing FNAs-based probes and presents a streamlined method for the conceptualization and optimization of DNA nanodevices.

Enzyme-Free Dynamic DNA Reaction Networks for On-Demand Bioanalysis and Bioimaging

ConspectusThe pursuit of in-depth studying the nature and law of life activity has been dominating current research fields, ranging from fundamental biological studies to applications that concern synthetic biology, bioanalysis, and clinical diagnosis. Motivated by this intention, the spatiotemporally controlled and in situ analysis of living cells has been a prospective branch by virtue of high-sensitivity imaging of key biomolecules, such as biomarkers. The past decades have attested that deoxyribonucleic acid (DNA), with biocompatibility, programmability, and customizable features, is a competitive biomaterial for constructing high-performance molecular sensing tools. To conquer the complexity of the wide extracellular-intracellular distribution of biomarkers, it is a meaningful breakthrough to explore high-efficiently amplified DNA circuits, which excel at operating complex yet captivating dynamic reaction networks for various bioapplications. In parallel, the multidimensional performance improvements of nucleic acid circuits, including the availability, detection sensitivity, and reliability, are critical parameters for realizing accurate imaging and cell regulation in bioanalysis.In this Account, we summarize our recent work on enzyme-free dynamic DNA reaction networks for bioanalysis from three main aspects: DNA circuitry functional extension of molecular recognition for epigenetic analysis and regulation, DNA circuitry amplification ability improvement for sensitive biomarker detection, and site-specific activation of DNA circuitry systems for reliable and accurate cell imaging. In the first part, we have designed an epigenetically responsive deoxyribozyme (DNAzyme) circuitry system for intracellular imaging and gene regulation, which enriches the possible analyzed species by chemically modifying conventional DNAzyme. For example, an exquisite N6-methyladenine (m6A)-caged DNAzyme was built for achieving the precise FTO (fat mass and obesity-associated protein)-directed gene regulation. In addition, varieties of DNAzyme-based nanoplatforms with self-sufficient cofactor suppliers were assembled, which subdued the speed-limiting hardness of DNAzyme cofactors in live-cell applications. In the second part, we have developed a series of hierarchically assembled DNA circuitry systems to improve the signal transduction ability of traditional DNA circuits. First, the amplification ability of the DNAzyme circuit has been significantly enhanced via several heterogeneously or homogeneously concatenated circuitry models. Furthermore, a feedback reaction pathway was integrated into these concatenated circuits, thus dramatically increasing the amplification efficiency. Second, considering the complex cellular environment, we have simplified the redundancy of multicomponents or reaction procedures of traditional cascaded circuits, relying on the minimal component complexity and merely one modular catalytic reaction, which guaranteed high cell-delivering uniformity while fostering reaction kinetics and analysis reliability. In the third part, we have constructed in-cell-selective endogenous-stimulated DNA circuitry systems via the multiply guaranteed molecular recognitions, which could not only eliminate the signal leakage, but could also retain its on-site and multiplex signal amplification. Based on the site-specific activation strategy, more circuitry availability in cellular scenarios has been acquired for reliable and precise biological sensing and regulation. These enzyme-free dynamic DNA reaction networks demonstrate the purpose-to-concreteness engineering for tailored multimolecule recognition and multiple signal amplification, achieving high-gain signal transduction and high-reliability targeted imaging in bioanalysis. We envision that the enzyme-free dynamic DNA reaction network can contribute to more bioanalytical layouts, which will facilitate the progression of clinical diagnosis and prognosis.

Spatiotemporally Programmed Disassembly of Multifunctional Integrated DNAzyme Nanoplatfrom for Amplified Intracellular MicroRNA Imaging

The sensing performance of DNAzymes in live cells is tremendously hampered by the inefficient and inhomogeneous delivery of DNAzyme probes and their incontrollable off-site activation, originating from their susceptibility to nuclease digestion. This requires the development of a more compact and robust DNAzyme-delivering system with site-specific DNAzyme activation property. Herein, a highly compact and robust Zn@DDz nanoplatform is constructed by integrating the unimolecular microRNA-responsive DNA-cleaving DNAzyme (DDz) probe with the requisite DNAzyme Zn2+ -ion cofactors, and the amplified intracellular imaging of microRNA via the spatiotemporally programmed disassembly of Zn@DDz nanoparticles is achieved. The multifunctional Zn@DDz nanoplatform is simply composed of a structurally blocked self-hydrolysis DDz probe and the inorganic Zn2+ -ion bridge, with high loading capacity, and can effectively deliver the initially catalytic inert DDz probe and Zn2+ into living cells with enhanced stabilities. Upon their entry into the acidic microenvironment of living cells, the self-sufficient Zn@DDz nanoparticle is disassembled to release DDz probe and simultaneously supply Zn2+ -ion cofactors. Then, endogenous microRNA-21 catalyzes the reconfiguration and activation of DDz for generating the amplified readout signal with multiply guaranteed imaging performance. Thus, this work paves an effective way for promoting DNAzyme-based biosensing systems in living cells, and shows great promise in clinical diagnosis.

Rational Engineering of a Multifunctional DNA Assembly for Enhanced Antibacterial Efficacy and Accelerated Wound Healing

DNA-based assemblies hold immense prospects for antibacterial application, yet are constrained by their poor specificity and deficient antibacterial delivery. Herein, the fabrication of a versatile rolling circle amplification (RCA)-sustained DNA assembly is reported, encoding simultaneously with multivalent aptamers and tandem antibacterial agents, for target-specific and efficient antibacterial application. In the compact RCA-sustained antibacterial platform, the facilely organized multivalent aptamers guarantee the target bacteria-specific delivery of sufficient antibacterial agents which is assembled through DNA-stabilizing silver nanostructures. It is shown that the biocompatible DNA system could enhance bacteria elimination and simultaneously facilitate wound healing in vivo. By virtue of the programmable RCA assembly, the present RCA-sustained system provides a highly modular and scalable approach to design versatile multifunctional therapeutic systems.

A Self-Immolative DNA Nanogel Vaccine toward Cancer Immunotherapy

The development of precisely engineered vehicles for intracellular delivery and the controlled release of payloads remains a challenge. DNA-based nanomaterials offer a promising solution based on the A-T-G-C alphabet-dictated predictable assembly and high programmability. Herein, we present a self-immolative DNA nanogel vaccine, which can be tracelessly released in the intracellular compartments and activate the immune response. Three building blocks with cytosine-rich overhang domains are designed to self-assemble into a DNA nanogel framework with a controlled size. Two oligo agonists and one antigen peptide are conjugated to the building blocks via an acid-labile chemical linker. Upon internalization into acidic endosomes, the formation of i-motif configurations leads to dissociation of the DNA nanogel vaccine. The acid-labile chemical linker is cleaved, releasing the agonists and antigen in their traceless original form to activate antigen-presenting cells and an immune response. This study presents a novel strategy for constructing delivery platforms for intracellularly stimuli-triggered traceless release of therapeutics.

Tunable metal-organic frameworks assist in catalyzing DNAzymes with amplification platforms for biomedical applications

Various binding modes of tunable metal organic frameworks (MOFs) and functional DNAzymes (Dzs) synergistically catalyze the emergence of abundant functional nanoplatforms. Given their serial variability in formation, structural designability, and functional controllability, Dzs@MOFs tend to be excellent building blocks for the precise "intelligent" manufacture of functional materials. To present a clear outline of this new field, this review systematically summarizes the progress of Dz integration into MOFs (MOFs@Dzs) through different methods, including various surface infiltration, pore encapsulation, covalent binding, and biomimetic mineralization methods. Atomic-level and time-resolved catalytic mechanisms for biosensing and imaging are made possible by the complex interplay of the distinct molecular structure of Dzs@MOF, conformational flexibility, and dynamic regulation of metal ions. Exploiting the precision of DNAzymes, MOFs@Dzs constructed a combined nanotherapy platform to guide intracellular drug synthesis, photodynamic therapy, catalytic therapy, and immunotherapy to enhance gene therapy in different ways, solving the problems of intracellular delivery inefficiency and insufficient supply of cofactors. MOFs@Dzs nanostructures have become excellent candidates for biosensing, bioimaging, amplification delivery, and targeted cancer gene therapy while emphasizing major advancements and seminal endeavors in the fields of biosensing (nucleic acid, protein, enzyme activity, small molecules, and cancer cells), biological imaging, and targeted cancer gene delivery and gene therapy. Overall, based on the results demonstrated to date, we discuss the challenges that the emerging MOFs@Dzs might encounter in practical future applications and briefly look forward to their bright prospects in other fields.

Self-Powered Biosensor Based on DNA Walkers for Ultrasensitive MicroRNA Detection

A novel self-powered biosensor is fabricated for ultrasensitive microRNA-21 (miRNA-21) detection, which includes an enzymatic biofuel cell (EBFC), DNA walkers, a digital multimeter (DMM), and a capacitor. As a novel strategy for signal amplification, DNA walkers are designed in the cathode, while the capacitor stores electrochemical energy from the EBFC to further boost the instantaneous current displayed by the DMM. When miRNA-21 is present, the DNA walkers are provoked to walk from as-opened hairpin structures to other hairpin structures, generating double-strand DNA structures, which stimulate [Ru(NH3)6]3+ to be adsorbed on the cathode surface by electrostatic interaction. Afterward, [Ru(NH3)6]3+ is reduced to [Ru(NH3)6]2+, and the open circuit voltage (EOCV) is significantly increased. Depending on the approach of signal amplification from DNA walkers, this biosensor displays an ultrasensitive assay toward miRNA-21 in the range of 0.5 to 104 fM, with a detection limit of 0.15 fM. In addition, this self-powered biosensor displays high selectivity for miRNA-21 assay in human serum samples.

Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors

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

A Smart Deoxyribozyme-Programmable Catalytic DNA Circuit for High-Contrast MicroRNA Imaging

Synthetic catalytic DNA circuits have been recognized as a promising signal amplification toolbox for sensitive intracellular imaging, yet their selectivity and efficiency are always constrained by uncontrolled off-site signal leakage and inefficient on-site circuitry activation. Thus, the endogenously controllable on-site exposure/activation of DNA circuits is highly desirable for achieving the selective imaging of live cells. Herein, an endogenously activated DNAzyme strategy was facilely integrated with a catalytic DNA circuit for guiding the selective and efficient microRNA imaging in vivo. To prevent the off-site activation, the circuitry constitute was initially caged without sensing functions, which could be selectively liberated by DNAzyme amplifier to guarantee the high-contrast microRNA imaging in target cells. This intelligent on-site modulation strategy can tremendously expand these molecularly engineered circuits in biological systems.