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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., (© 2024 Wiley-VCH GmbH.)

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., (© 2023 Wiley-VCH GmbH.)

The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed., (© 2023 Wiley-VCH GmbH.)

A versatile approach for the fine control of DNA-based hierarchical assembly via dual stimuli and two assembly strategies is developed. Moreover, with a reasonable design of functional thrombin aptamer structures on the formed DNA nanoassembly, it can achieve precise regulation of thrombin activity.

The epigenetic modification of nucleic acids represents a versatile approach for achieving high-efficient control over gene expression and transcription and could dramatically expand their biosensing and therapeutic applications. Demethylase-involved removal of N6-methyladenine (m 6 A) represents one of the vital epigenetic reprogramming events, yet its direct intracellular evaluation and as-guided gene regulation are extremely rare. The endonuclease-mimicking deoxyribozyme (DNAzyme) is a catalytically active DNA that enables the site-specific cleavage of the RNA substrate, and several strategies have imparted the magnificent responsiveness to DNAzyme by using chemical and light stimuli. However, the epigenetic regulation of DNAzyme has remained largely unexplored, leaving a significant gap in responsive DNA nanotechnology. Herein, we reported an epigenetically responsive DNAzyme system through the in vitro selection of an exquisite m 6 A-caged DNAzyme that could be specifically activated by FTO (fat mass and obesity-associated protein) demethylation for precise intracellular imaging-directed gene regulation. Based on a systematic investigation, the active DNAzyme configuration was potently disrupted by the site-specific incorporation of m 6 A modification and subsequently restored into the intact DNAzyme structure via the tunable FTO-specific removal of m 6 A-caging groups under a variety of conditions. This orthogonal demethylase-activated DNAzyme amplifier enables the robust and accurate monitoring of FTO and its inhibitors in live cells. Moreover, the simple demethylase-activated DNAzyme facilitates the assembly of an intelligent self-adaptive gene regulation platform for knocking down demethylase with the ultimate apoptosis of tumor cells. As a straightforward and scarless m 6 A removal strategy, the demethylase-activated DNAzyme system offers a versatile toolbox for programmable gene regulation in synthetic biology.

Nucleic acids are considered not only extraordinary carriers of genetic information but also are perceived as the perfect elemental materials of molecular recognition and signal transduction/amplification for assembling programmable artificial reaction networks or circuits, which are similar to conventional electronic logic devices. Among these sophisticated DNA-based reaction networks, catalytic hairpin assembly (CHA), hybridization chain reaction (HCR), and DNAzyme represent the typical nonenzymatic amplification methods with high robustness and efficiency. Furthermore, their extensive hierarchically cascade integration into multi-layered autonomous DNA circuits establishes novel paradigms for constructing more different catalytic DNA nanostructures and for regenerating or replicating diverse molecular components with specific functions. Various DNA and inorganic nanoscaffolds have been used to realize the surface-confined DNA reaction networks with significant biomolecular sensing and signal-regulating functions in living cells. Especially, the specific aptamers and metal-ion-bridged duplex DNA nanostructures could extend their paradigms for detecting small molecules and proteins in even living entities. Herein, the varied enzyme-free DNA circuits are introduced in general with an extensive explanation of their underlying molecular reaction mechanisms. Challenges and outlook of the autonomous enzyme-free DNA circuits will also be discussed at the end of this chapter.

The development of self-assembled DNA nanomedicine requires a facile and accurate DNA degradation strategy for precisely programmable drug release. Conventional DNA catabolic strategies are restrained with the fragile and unclear enzymatic reactions that might lead to inefficient and uncontrollable digestion of DNA scaffolds and thus might bring undesirable side effects to the sophisticated biosystems. Herein we reported a versatile self-sufficient DNAzyme-driven drug delivery system consisting of the rolling circle polymerized DNAzyme-substrate scaffolds and the encapsulated pH-responsive ZnO nanoparticles (NPs). The full DNAzyme nanosponges (NSs) were also encoded with multivalent tandem aptamer sequences to facilitate their efficient delivery into cancer cells, where the acidic endo/lysosomal microenvironment stimulates the dissolution of ZnO into Zn 2+ ions as DNAzyme cofactors and therapeutic reactive oxygen species generators. The supplement Zn 2+ cofactors mediated the nonviolent DNAzyme-catalyzed cleavage of DNA scaffolds for precise and efficient drug administrations with synergistically enhanced therapeutic performance. The facile design of DNAzyme, together with their cost-effective and intrinsic robust features, is anticipated to provide extensive insights for the development of DNA-based therapeutic platforms by activating the specific intracellular biocatalytic reactions. As an intelligent and nonviolent self-driven drug delivery platform, the present DNAzyme NS system could be engineered with more therapeutic sequences and agents and was anticipated to show exceptional promise and versatility for applications in biomedicine and bioengineering.

Isothermal enzyme-free nucleic acid circuits have been developed for carrying out diverse functions ranging from dictate biocomputing to amplified biosensing. Catalytic hairpin assembly (CHA), the catalyzed cross-opening of two hairpin substrates by an initiator, has attracted increasing attention because of its facile design and high amplification capacity. The complex labeling and frequent photobleaching of a conventional fluorescent CHA biosensor still remains a challenge that needs to be solved. Herein, we constructed a new label-free and enzyme-free isothermal CHA lighting up AgNCs strategy for amplified nucleic acid assay by integrating the interfacially and spatially sensitive feature of DNA-templated fluorescent silver nanoclusters (DNA-AgNCs) and the high signal amplification capability of the CHA circuit. In this strategy, one polyguanine-grafted hairpin and the other AgNCs-capturing hairpin were engineered as assembly constitutes, which were kinetically impeded from cross-hybridizations without target. However, in the presence of target, the CHA-catalyzed assembly of two functional hairpins was successively progressed and concomitantly accompanied by an efficient accommodation of AgNCs to the polyguanine-elongated dsDNA product, leading to highly efficient AgNCs-lighting up and to the generation of an amplified fluorescence signal. As a simple mix-and-detect strategy, the isothermal enzyme-free CHA-mediated lighting up AgNCs (CHA-AgNCs) system provided a facile visualization way for amplified detection of DNA with a detection limit of 20 pM, which was comparable to or even better than some enzyme-involved amplification methods. The homogeneous CHA-AgNCs system can be used as a general sensing platform and be easily adapted for analyzing other biologically important analytes, for example, microRNA (miRNA), by introducing the sensing module consisting of an auxiliary hairpin through an easy-to-integrate procedure. By taking advantage of the signal amplification features of CHA and the robust AgNCs-lighting up procedure, we anticipate that the CHA-lighting up AgNCs system can provide an important tool for biomedicine and bioimaging applications and thus should hold great promise in clinical diagnoses and treatment fields.

An autonomous nonenzymatic DNA machine has been successfully engineered based on a two-layered cascaded hybridization chain reaction (C-HCR) circuit, in which the tandem outputs of the upstream HCR-1 unit activate the downstream HCR-2 unit to induce successive repeated hybridizations, generating branched DNA structures and enabling sensitive and selective detection of uracil-DNA glycosylase and its inhibitors.

Cytosolic DNA-mediated activation of the transcription factor IRF3 is a key event in host antiviral responses. Here we found that infection with DNA viruses induced interaction of the metabolic checkpoint kinase mTOR downstream effector and kinase S6K1 and the signaling adaptor STING in a manner dependent on the DNA sensor cGAS. We further demonstrated that the kinase domain, but not the kinase function, of S6K1 was required for the S6K1-STING interaction and that the TBK1 critically promoted this process. The formation of a tripartite S6K1-STING-TBK1 complex was necessary for the activation of IRF3, and disruption of this signaling axis impaired the early-phase expression of IRF3 target genes and the induction of T cell responses and mucosal antiviral immunity. Thus, our results have uncovered a fundamental regulatory mechanism for the activation of IRF3 in the cytosolic DNA pathway.

Acrylamide/acrylamide-modified nucleic acid copolymer chains provide building units for the construction of acrylamide-DNA hydrogels. Three different hydrogels are prepared by the cross-linking of the acrylamide-DNA chains with metal ion-dependent DNAzyme sequences and their substrates. The metal ion-dependent DNAzyme sequences used in the study include the Cu(2+)-, Mg(2+)-, and Zn(2+)-dependent DNAzymes. In the presence of the respective metal ions, the substrates of the respective DNAzymes are cleaved, leading to the separation of the cross-linking units and to the dissolution of the hydrogel. The different hydrogels were loaded with a fluorophore-modified dextran or with a fluorophore-functionalized glucose oxidase. Treatment of the different hydrogels with the respective ions led to the release of the loaded dextran or the enzyme, and the rates of releasing of the loaded macromolecules followed the order of Cu(2+) > Mg(2+) > Zn(2+). Also, the different hydrogels were loaded with the enzymes β-galactosidase (β-Gal), glucose oxidase (GOx), or horseradish peroxidase (HRP). In the presence of the appropriate metal ions, the respective hydrogels were dissolved, resulting in the activation of the β-Gal/GOx or GOx/HRP bienzyme cascades and of the β-Gal/GOx/HRP trienzyme cascade.

Nucleic acid-functionalized polyacrylamide chains that are cooperatively cross-linked by i-motif and nucleic acid duplex units yield, at pH 5.0, DNA hydrogels exhibiting shape-memory properties. Separation of the i-motif units at pH 8.0 dissolves the hydrogel into a quasi-liquid phase. The residual duplex units provide, however, a memory code in the quasi-liquid allowing the regeneration of the hydrogel shape at pH 5.0., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Luminescent nucleic acid-stabilized Ag nanoclusters (Ag NCs) are applied for the optical detection of DNA and for the multiplexed analysis of genes. Two different sensing modules including Ag NCs as luminescence labels are described. One sensing module involves the assembly of a three-component sensing module composed of a nucleic acid-stabilized Ag NC and a quencher-modified nucleic acid hybridized with a nucleic acid scaffold that is complementary to the target DNA. The luminescence of the Ag NCs is quenched in the sensing module nanostructure. The strand displacement of the scaffold by the target DNA separates the nucleic acid-functionalized Ag NCs, leading to the turned-on luminescence of the NCs and to the optical readout of the sensing process. By implementing two different-sized Ag NC-modified sensing modules, the parallel multiplexed analysis of two genes (the Werner Syndrome gene and the HIV, human immunodeficiency, gene), using 615 and 560 nm luminescent Ag NCs, is demonstrated. The second sensing module includes the nucleic acid functionalized Ag NCs and the quencher-modified nucleic acid hybridized with a hairpin DNA scaffold. The luminescence of the Ag NCs is quenched in the sensing module. Opening of the hairpin by the target DNA triggers the luminescence of the Ag NCs, due to the spatial separation of the Ag NCs/quencher units. The system is applied for the optical detection of the BRAC1 gene. In addition, by implementing two-sized Ag NCs, the multiplexed analysis of two genes by the hairpin sensing module approach is demonstrated.

The amplified, highly sensitive detection of DNA using the dendritic rolling circle amplification (RCA) is introduced. The analytical platform includes a circular DNA and a structurally tailored hairpin structure. The circular nucleic acid template includes a recognition sequence for the analyte DNA (the Tay-Sachs mutant gene), a complementary sequence to the Mg(2+)-dependent DNAzyme, and a sequence identical to the loop region of the coadded hairpin structure. The functional hairpin in the system consists of the analyte-sequence that is caged in the stem region and a single-stranded loop domain that communicates with the RCA product. The analyte activates the RCA process, leading to DNA chains consisting of the Mg(2+)-dependent DNAzyme and sequences that are complementary to the loop of the functional hairpin structure. Opening of the coadded hairpin releases the caged analyte sequence, resulting in the dendritic RCA-induced synthesis of the Mg(2+)-dependent DNAzyme units. The DNAzyme-catalyzed cleavage of a fluorophore/quencher-modified substrate leads to a fluorescence readout signal. The method enabled the analysis of the target DNA with a detection limit corresponding to 1 aM. By the design of two different circular DNAs that include recognition sites for two different target genes, complementary sequences for two different Mg(2+)-dependent DNAzyme sequences and two different functional hairpin structures, the dendritic RCA-stimulated multiplexed analysis of two different genes is demonstrated. The amplified dendritic RCA detection of DNA is further implemented to yield the hemin/G-quadruplex horseradish peroxidase (HRP)-mimicking DNAzyme as catalytic labels that provide colorimetric or chemiluminescent readout signals.

The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

DNA-gated mesoporous SiO2 nanoparticles, MP-SiO2 NPs, loaded with rhodamine B, RhB, act as "smart" materials that reveal complementary "sense" and "release" functionalities. The unlocking of the DNA pore-capping units is achieved by the biocatalytic cleavage of the DNA, and the unlocking process is amplified by the regeneration of the analyte-trigger. The RhB-loaded MP-SiO2 NPs are capped with nucleic acid hairpin structures that lock the RhB in the pores. Opening of the hairpin structures by a nucleic acid analyte trigger or by the formation of an aptamer-substrate (ATP) complex leads to the formation of duplex structures being cleaved by exonuclease III, Exo III, or the nicking enzyme, Nb. BbvCI. This results in the regeneration of the target analytes, the autonomous unlocking of the pores, and the release of RhB. The systems reveal selectivity, and one-, two-, three-base mutations in the target DNA, or substitution of ATP with other triphosphate nucleotides, prohibit the unlocking of the pores. In analogy to the biocatalytic release of the model fluorophore substrates, the anticancer drug camptothecin, CPT, was entrapped in the pores and locked by the 1 or 11 hairpin structures. The drug was released from the pores in the presence of the nucleic acid 2 or ATP and the Exo III, as biocatalyst. Similarly, CPT locked in the pores by the 6 or 12 hairpins were released from the pores in the presence of ATP and Nb. BbvCI, as nicking enzyme, respectively. The effects of the CPT-loaded MP-SiO2 NPs, capped with the ATP-dependent lock 6, on the viability of MDA-231 breast cancer cells and MCF-10a normal breast cells were examined. We find that after 48 h, 65% cell death was observed for the MDA-231 cancer cells, where only 25% cell death was observed for the normal cells. The higher cell death of the cancer cells correlates well with the enhanced metabolic synthesis of ATP in the cancerous cells.

Two different methods to self-assemble red- or yellow-luminescent nucleic acids-stabilized Ag nanoclusters (NCs) nanowires are presented. By one method, the autonomous hybridization-polymerization process between two nucleic acids leads to polymer chains consisting of sequence-specific loops for the stabilization of the red- or yellow-emitting Ag NCs. By the other method, the nucleic acid-triggered hybridization chain reaction (HCR) involving the cross-opening of two functional hairpins leads to sequence-specific DNA loops and a nucleic acid scaffold that stabilize the respective red- or yellow-emitting Ag NCs. The micrometer-long luminescent Ag NC-functionalized nanowires are imaged by AFM and confocal microscopy.

Hybrid systems consisting of nucleic-acid-functionalized silver nanoclusters (AgNCs) and graphene oxide (GO) are used for the development of fluorescent DNA sensors and aptasensors, and for the multiplexed analysis of a series of genes of infectious pathogens. Two types of nucleic-acid-stabilized AgNCs are used: one type includes the red-emitting AgNCs (616 nm) and the second type is near-infrared-emitting AgNCs (775 nm). Whereas the nucleic-acid-stabilized AgNCs do not bind to GO, the conjugation of single-stranded nucleic acid to the DNA-stabilized AgNCs leads to the adsorption of the hybrid nanostructures to GO and to the fluorescence quenching of the AgNCs. By the conjugation of oligonucleotide sequences acting as probes for target genes, or as aptamer sequences, to the nucleic-acid-protected AgNCs, the desorption of the probe/nucleic-acid-stabilized AgNCs from GO through the formation of duplex DNA structures or aptamer-substrate complexes leads to the generation of fluorescence as a readout signal for the sensing events. The hybrid nanostructures are implemented for the analysis of hepatitis B virus gene (HBV), the immunodeficiency virus gene (HIV), and the syphilis (Treponema pallidum) gene. Multiplexed analysis of the genes is demonstrated. The nucleic-acid-AgNCs-modified GO is also applied to detect ATP or thrombin through the release of the respective AgNCs-labeled aptamer-substrate complexes from GO.

The information encoded in the base sequence of DNA provides substantial structural and functional information for the instructive self-assembly of one-dimensional (1D) functional DNA nanostructures. The hybridization chain reaction (HCR) and the formation of HCR-stimulated DNAzyme nanochains are presented, as a means to develop amplified DNA sensors and aptasensors. Similarly, the rolling circle amplification (RCA) process is implemented to generate 1D DNA nanochains consisting of constant repeat units being implemented for the amplified sensing (using DNAzymes as repeat units) and for the switchable control of electron transfer at electrodes. 1D DNA nanostructures are used as templates for the programmed positioning of enzymes that enable the activation of enzyme cascades and the biocatalytic growth of metallic nanowires. The future perspectives of the self-assembly mechanisms are discussed., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

DNA nanostructures acting as DNA machines are described. Specifically, DNA "walkers" assembled on nucleic acid scaffolds and triggered by fuel/antifuel strands are activated in solution or on surfaces, for example, electrodes or semiconductor CdSe/ZnS quantum dots (QDs). The DNA machines led to the switchable formation or dissociation of the hemin/G-quadruplex DNAzyme on the DNA scaffolds. This enabled the chemiluminescence, chemiluminescence resonance energy transfer (CRET), electrochemical, or photoelectrochemical transduction of the switchable states of the different DNA machines.

DNA-stabilized Ag nanoclusters, AgNCs, act as fluorescent labels for probing enzyme activities and their substrates. The effective quenching of AgNCs by H(2)O(2) enables the probing of H(2)O(2)-generating oxidases. This is demonstrated by following the glucose oxidase-stimulated oxidation of glucose through the enzyme-catalyzed formation of H(2)O(2). Similarly, the effective quenching of the AgNCs by quinones enabled the detection of tyrosinase through the biocatalyzed oxidation of tyrosine, dopamine, or tyramine to the respective quinone products. The sensitive probing of biocatalytic processes by the AgNCs was further implemented to follow bienzyme catalytic cascades involving alkaline phosphatase/tyrosinase and acetylcholine esterase/choline oxidase. The characterization of the alkaline phosphatase/tyrosinase cascade enabled the ultrasensitive detection of alkaline phosphatase (5 × 10(-5) units/mL) and the detection of o-phospho-l-tyrosine that is an important intracellular promoter and control growth factor.

Polymerase/nicking enzymes and nucleic-acid scaffolds are implemented as DNA machines for the development of amplified DNA-detection schemes, and for the design of logic gates. The analyte nucleic acid target acts, also, as input for the logic gates. In the presence of two DNA targets, acting as inputs, and appropriate DNA scaffolds, the polymerase-induced replication of the scaffolds, followed by the nicking of the replication products, are activated, leading to the autonomous synthesis of the Mg(2+)-dependent DNAzyme or the Mg(2+)-dependent DNAzyme subunits. These biocatalysts cleave a fluorophore/quencher-functionalized nucleic-acid substrate, thus providing fluorescence signals for the sensing events or outputs for the logic gates. The systems are used to develop OR, AND, and Controlled-AND gates, and the DNA-analyte targets represent two nucleic acid sequences of the smallpox viral genome., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A generic fluorescence sensing platform for analyzing DNA by the Zn(2+)-dependent ligation DNAzyme as amplifying biocatalyst is presented. The platform is based on the target DNA induced ligation of two substrate subunits and the subsequent opening of a beacon hairpin probe by the ligated product. The strand displacement of the ligated product by the beacon hairpin is, however, of limited efficiency. Two strategies are implemented to overcome this limitation. By one method, a "helper" nucleic acid sequence is introduced into the system, and this hybridizes with the DNAzyme components and releases the ligated product for opening of the hairpin. By the second method, a nicking enzyme (Nt.BspQI) is added to the system, and this nicks the duplex between the beacon and ligated product while recycling the free ligation product. By combining the two coadded components ("helper" sequence and nicking enzyme), the sensitive detection of the analyte is demonstrated (detection limit, 20 pM). The enzyme-free amplified fluorescence detection of the target DNA is further presented by the Zn(2+)-dependent ligation DNAzyme-driven activation of the Mg(2+)-dependent DNAzyme. According to this method, the Mg(2+)-dependent DNAzyme subunits displace the ligated product, and the resulting assembled DNAzyme cleaves a fluorophore/quencher-modified substrate to yield fluorescence. The method enabled the detection of the target DNA with a detection limit corresponding to 10 pM. The different sensing platforms are implemented to detect the Tay-Sachs genetic disorder mutant.

The Zn(2+)-dependent ligation DNAzyme is implemented as a biocatalyst for the amplified detection of a target DNA by the autonomous replication of a nucleic acid reporter unit that is generated by the catalyzed ligation process. The reporter units enhance the formation of active DNAzyme units, thus leading to the isothermal autocatalytic formation of the reporter elements. The system was further developed and applied for the amplified detection of Tay-Sachs genetic disorder mutant, with a detection limit of 1.0 × 10(-11) M. Besides providing a versatile paradigm for the amplified detection of DNA, the system reveals a new, enzyme-free, isothermal, autocatalytic mechanism that introduces means for effective programmed synthesis.

An enzyme-free amplified detection platform is described using the horseradish peroxidase (HRP)-mimicking DNAzyme as an amplifying label. Two hairpin structures that include three-fourths and one-fourth of the HRP-mimicking DNAzyme in caged, inactive configurations are used as functional elements for the amplified detection of the target DNA. In the presence of the analyte DNA, one of the hairpins is opened, and this triggers the autonomous cross-opening of the two hairpins using the strand displacement principle. This leads to the formation of nanowires consisting of the HRP-mimicking DNAzyme. The resulting DNA nanowires act as catalytic labels for the colorimetric or chemiluminescent readout of the sensing processes (the term "enzyme-free" refers to a protein-free catalyst). The analytical platform allows the sensing of the analyte DNA with a detection limit corresponding to 1 × 10(-13) M. The optimized system acts as a versatile sensing platform, and by coaddition of a "helper" hairpin structure any DNA sequence may be analyzed by the system. This is exemplified with the detection of the BRCA1 oncogene with a detection limit of 1 × 10(-13) M.

A systematic study of the amplified optical detection of DNA by Mg(2+)-dependent DNAzyme subunits is described. The use of two DNAzyme subunits and the respective fluorophore/quencher-modified substrate allows the detection of the target DNA with a sensitivity corresponding to 1 × 10(-9) M. The use of two functional hairpin structures that include the DNAzyme subunits in a caged, inactive configuration leads, in the presence of the target DNA, to the opening of one of the hairpins and to the activation of an autonomous cross-opening process of the two hairpins, which affords polymer DNA wires consisting of the Mg(2+)-dependent DNAzyme subunits. This amplification paradigm leads to the analysis of the target DNA with a sensitivity corresponding to 1 × 10(-14) M. The amplification mixture composed of the two hairpins can be implemented as a versatile sensing platform for analyzing any gene in the presence of the appropriate hairpin probe. This is exemplified with the detection of the BRCA1 oncogene.

In this work, we illustrate a simple chelation-based strategy to trigger DNA release from DNA-incorporated multilayer films, which were fabricated through the layer-by-layer (LbL) assembly of DNA and inorganic zirconium (IV) ion (Zr(4+)). After being incubated in several kinds of chelator solutions, the DNA multilayer films disassembled and released the incorporated DNA. This was most probably due to the cleavage of coordination/electrostatic interactions between Zr(4+) and phosphate groups of DNA. Surface plasmon resonance (SPR), UV-vis spectrometry and atomic force microscopy (AFM) were used to characterize the assembly and the disassembly of the films. By incorporating plasmid DNA (pDNA) into this controllable disassembly system, the multilayer films sustained the consecutive DNA release. The released pDNA retained its integrity and transcriptional activity, and also expressed enhanced green fluorescent protein (EGFP) after being transfected into HEK 293 cells. Besides the simplicity and cost efficiency of this method, the most advantage of this route was that the release of DNA from the films could be modulated by various external conditions, such as the chelator and ionic strength. The Zr(4+)/DNA multilayer films with the ability to precisely control the release rate of DNA might serve as an alternative localized gene delivery system in the perspective of biomedical applications.

A layer-by-layer film composed of DNA and inorganic zirconium ion (Zr(4+)) was fabricated on the surface of gold thin film, and an electric field triggered disintegration of the multilayer film was studied by using electrochemical surface plasmon resonance (EC-SPR). EC-SPR results demonstrated that the film was disassembled upon the application of an electric field and the disassembly rate varied with the applied potential, leading to the controlled release of DNA. The electrodissolution could be switched off by removing the electric potential and reactivated by reapplying the potential. By incorporating plasmid DNA (pDNA) in to this controlled release system, the multilayer film could sustain the consecutive release of pDNA electrochemically. The released pDNA retained its integrity and transfection activity, and expressed enhanced green fluorescent protein (EGFP) after being transfected into HEK 293 cells. The electrochemical systems, with advantages of miniaturization, surface-tailoring, safety, simplicity, convenience, automation, low-cost, and free of immune reactions, made the electrical route a very attractive gene-delivery alternative.

Through electrostatic layer-by-layer (LbL) assembly, negatively charged calf thymus double stranded DNA (CTds-DNA), and positively charged Zr4+ ions were alternately deposited on gold substrate modified with chemisorbed cysteamine. Thus-prepared three-dimensional DNA networks were characterized by surface plasmon resonance (SPR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and infrared reflection-absorption spectroscopy (IR-RAS). SPR spectroscopy indicates that the effective thickness of DNA monolayer in the (DNA/Zr4+)(1) bilayer was 1.5+/-0.1 nm, which corresponds to the surface coverage of 79% of its full packed monolayer. At the same time, a linear increase of film thickness with increasing number of layers was also confirmed by SPR characterizations. The data of XPS and IR-RAS show that Zr4+ ions interact with both the phosphate groups and nitrogenous bases of DNA and load into the framework of DNA. Furthermore, the interactions between this composite film and heme protein cytochrome c (Cyt c) were investigated by SPR spectroscopy and electrochemistry. Compared with the adsorption of Cyt c on DNA monolayer, this composite multilayer film can obviously enhance the amount of immobilized Cyt c confirmed by SPR reflectivity-incident angle (R-theta) curves. Cyclic voltammetry (CV) indicates the Cyt c adsorbed on the composite film is electroactive, and the enhancement of peak current in CV indirectly verifies the increase of the amount of immobilized Cyt c.

Synthetic biochemical circuits (e.g., DNA circuits) remain at the forefront of intracellular biosensing tasks yet are hindered by the undesired off‐site activation and the accompanying signal leakage. Herein, the study attempts to overcome this limitation by developing a simple‐yet‐powerful endogenous glutathione (GSH)‐regulating tactic that permits robust and distinguishable on‐site microRNA (miRNA) imaging under disturbed redox homeostasis. Specifically, a hierarchically activated catalytic DNA (HAD) circuit is fabricated by grafting the disulfide linkage within entropy‐driven DNA circuitry (EDC) reactants. It is exemplified that this HAD system promises the spatiotemporally selective microRNA‐21 (miR‐21) imaging in living cells and the robust differentiation of tumor cells from normal cells. The correlationship between GSH and miRNA is extensively explored in live cells, and can substantially expand the toolbox of DNA circuits for profiling intracellular biochemical processes. [ABSTRACT FROM AUTHOR]

Non‐invasive cell regulation represents a promising approach for on‐site cell modulation, but is confronted with inaccuracy or poor cell selectivity. Herein, by virtue of the interfacial‐activated concatenate DNA circuit, an activated recombination‐to‐modulation (ARM) machinery is developed to achieve accurate membrane imaging and effective cell modulation. Bioorthogonal signal transduction through the catalytic hairpin assembly circuit can continuously regenerate triggers for activating the subsequent circuit, with no activator consumption and occupation. The ARM strategy utilizes the amplified hybridization chain reaction to sensitively rearrange membrane receptors for blocking the related signaling pathways and indirectly modulating cell behaviors. Based on these two membrane receptor inputs, the controllably‐activated ARM strategy enables the identification of target cells among similar interfering cells with high accuracy and sensitivity. This machinery has demonstrated good performance in the efficient inhibition of tumor metastasis via the disruption of HGF/c‐Met‐signaling pathway. The modular‐designed ARM machinery provides a general platform for non‐invasive and specific cell modulation, suggesting a broad opportunity for advanced exploration of cellular metabolism behaviors. [ABSTRACT FROM AUTHOR]

Herein, we developed a reliable and portable biosensor (TDR-PGM nanomachine) for the sensitive detection of microRNA by integrating an efficient toehold-mediated strand displacement reaction module (TDR) and a personal glucose meter (PGM). The system provides a versatile methodology for microRNA detection in real samples and holds broad prospects in point-of-care diagnosis. [ABSTRACT FROM AUTHOR]

Lowly expressed analyte in complex cytoplasmic milieu necessitates the development of non‐enzymatic autocatalytic DNA circuits with high amplification and anti‐interference performance. Herein, we engineered a versatile and robust stimuli‐responsive autocatalytic hybridization assembly (AHA) circuit for high‐performance in vivo bioanalysis. Under a moderately confined condition, the initiator motivated the autonomous and cooperative cross‐activation of cascade hybridization reaction and catalytic DNA assembly for generating an exponentially amplified readout without the parasite steric hindrance and random diffusion side effects. The AHA circuit was systematically investigated by a series of experimental studies and theoretical simulations. The successively guaranteed target recognition and synergistically accelerated signal‐amplification enabled the sensitive and selective detection of analyte, and realized the robust miRNA imaging in living cells and mice. This autocatalytic DNA circuit could substantially expand the toolbox for accurate diagnosis and programmable therapeutics. [ABSTRACT FROM AUTHOR]

DNA nanostructures have recently attracted increasing interest in biological and biomedical applications by virtue of their unique properties, such as structural programmability, multi‐functionality, stimuli‐responsive behaviors, and excellent biocompatibility. In particular, the intelligent responsiveness of smart DNA nanostructures to specific stimuli has facilitated their extensive development in the field of high‐performance biosensing and controllable drug delivery. This minireview begins with different self‐assembly strategies for the construction of various DNA nanostructures, followed by the introduction of a variety of stimuli‐responsive functional DNA nanostructures for assembling metastable soft materials and for facilitating amplified biosensing. The recent achievements of smart DNA nanostructures for controllable drug delivery are highlighted. Finally, the current challenges and possible developments of this promising research are discussed in the fields of intelligent nanomedicine. [ABSTRACT FROM AUTHOR]

The therapeutic performance of DNAzyme‐involved gene silencing is significantly constrained by inefficient conditional activation and insufficient cofactor supply. Herein, a self‐sufficient therapeutic nanosystem was realized through the delicate design of DNAzyme prodrugs and MnO2 into a biocompatible nanocapsule with tumor‐specific recognition/activation features. The indocyanine green (ICG)‐modified DNA prodrugs are designed by splitting the DNAzyme and then reconstituted into the exquisite catalyzed hairpin assembly (CHA) amplification circuit. Based on the photothermal activation of ICG, the nanocapsule was disassembled to expose the MnO2 ingredient which was immediately decomposed into Mn2+ ions to supplement an indispensable DNAzyme cofactor on‐demand with a concomitant O2 generation for enhancing the auxiliary phototherapy. The endogenous microRNA catalyzes the amplified assembly of DNA prodrugs via an exquisite CHA principle, leading to the DNAzyme‐mediated simultaneous silencing of two key tumor‐involved mRNAs. This self‐activated theranostic nanocapsule could substantially expand the toolbox for accurate diagnosis and programmable therapeutics. [ABSTRACT FROM AUTHOR]

The activation of stimulator of interferon genes (STING) plays a key role for provoking effective innate and adaptive immunity, yet is constrained by the limited clinical translation of STING agonists. Herein, we construct a smart DNA sponge to deliver STING agonists for robust cancer immunotherapy via the synergistic activation of innate immune pathways. The compact DNA sponge (Mn-CpG), assembling through a simple rolling circle amplification reaction, is encoded with numerous STING agonist (Mn2+) and toll-like receptor 9 (TLR9) agonist (CpG oligodeoxynucleotide) and allows their on-demand cellular delivery We show that Mn-CpG sponge can trigger the synergistic type I interferon response and robust T cell priming through a convenient coordination of different signaling pathways. In a poorly immunogenic breast cancer model, the method achieves the boosted immune responses with significantly inhibited tumor growth and metastasis. [Display omitted] • The compact DNA sponge realizes the on-demand cellular delivery of STING and TLR9 agonists into antigen-presenting cells. • This system actualizes two innate immune stimuli to achieve effective antitumour immunity with decreased autoimmune toxicity. • It provides a simple yet powerful tactic that renders DNA-based STING activation with synergistic innate immunomodulation. [ABSTRACT FROM AUTHOR]

Abstract: The development of effective strategies for sensitive and specific detection of microRNAs will facilitate clinical diagnostics. Here, we utilize cascade hybridization chain reaction as an enzyme‐free isothermal amplified strategy, and construct label‐free electrochemical biosensors for microRNAassay. MicroRNA initiated autonomous assembly of DNA nanostructures through the toehold‐mediated strand displacement reaction. The assembly behavior was examined by gel electrophoresis and morphology of branched DNA nanostructure was verified by atomic force microscope. This cascade hybridization chain reaction leads to extended growth of DNA chains and higher amplification efficiency compared with the regular hybridization chain reaction. The performance of the sensors was characterized by electrochemical impedance spectroscopy, differential pulse voltammetry, and chronocoulometric analysis. The prepared biosensor exhibits high sensitivity and a lower detection limit of 11 pM for the determination of microRNA‐21. This electrochemical assay based on cascade hybridization chain reaction is specific and can distinguish between highly homologous targets such as fully complementary target microRNA‐21, single, or two‐base mismatched sequences and other family members. These findings open the possibility of using cascade hybridization chain reaction as possible amplified electrochemical sensing platforms. [ABSTRACT FROM AUTHOR]

DNA Circuit, Fluorescence, RNA, Signal Amplification, Tumor Imaging Der am Wirkort aktivierte CCD-Schaltkreis hat erhebliches Potenzial für die hochpräzise In-vivo-Bildgebung von microRNA. Keywords: DNA Circuit; Fluorescence; RNA; Signal Amplification; Tumor Imaging EN DNA Circuit Fluorescence RNA Signal Amplification Tumor Imaging 1 1 1 11/03/22 20221107 NES 221107 B Eine nicht-enzymatische b Aktivierungsstrategie mittels multipler molekularer Erkennungsereignisse und progressiv beschleunigter Signalverstärkung führte zu einem orthogonal gesteuerten katalytischen DNA-Schaltkreis (CCD), wie Fuan Wang et al. in ihrem Forschungsartikel berichten (e202206529). [Extracted from the article]

Mimicking cellular transformations and signal transduction pathways by means of biocatalytic cascades proceeding in organized media is a scientific challenge. We describe two DNA machines that enable the 'ON/OFF' switchable activation and deactivation of three-component biocatalytic cascades. One system consists of a reconfigurable DNA tweezers-type structure, whereas in the second system the catalytic cascade proceeds on a switchable DNA clamp scaffold. The three-component catalytic cascades consist of β-galactosidase (β-Gal), glucose oxidase (GOx), and the K+-ion-stabilized hemin-G-quadruplex horseradish peroxidase (HRP)-mimicking DNAzyme. The hemin-G-quadruplex-bridged closed structure of the tweezers or clamp allows the biocatalytic cascades to operate (switched 'ON′′), whereas separation of the hemin-G-quadruplex by means of 18-crown-6-ether opens the tweezers/clamp structures, thus blocking the catalytic cascade (switched 'OFF'). This study is complemented by two-component, switchable biocatalytic cascades composed of GOx and hemin-G-quadruplex assembled on hairpin-bridged DNA tweezers or clamp nanostructures. [ABSTRACT FROM AUTHOR]

Polymerase/nicking enzymes and nucleic-acid scaffolds are implemented as DNA machines for the development of amplified DNA-detection schemes, and for the design of logic gates. The analyte nucleic acid target acts, also, as input for the logic gates. In the presence of two DNA targets, acting as inputs, and appropriate DNA scaffolds, the polymerase-induced replication of the scaffolds, followed by the nicking of the replication products, are activated, leading to the autonomous synthesis of the Mg2+-dependent DNAzyme or the Mg2+-dependent DNAzyme subunits. These biocatalysts cleave a fluorophore/quencher-functionalized nucleic-acid substrate, thus providing fluorescence signals for the sensing events or outputs for the logic gates. The systems are used to develop OR, AND, and Controlled-AND gates, and the DNA-analyte targets represent two nucleic acid sequences of the smallpox viral genome. [ABSTRACT FROM AUTHOR]

Abstract: Through electrostatic layer-by-layer (LbL) assembly, negatively charged calf thymus double stranded DNA (CTds-DNA), and positively charged Zr4+ ions were alternately deposited on gold substrate modified with chemisorbed cysteamine. Thus-prepared three-dimensional DNA networks were characterized by surface plasmon resonance (SPR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and infrared reflection–absorption spectroscopy (IR-RAS). SPR spectroscopy indicates that the effective thickness of DNA monolayer in the (DNA/Zr4+)1 bilayer was 1.5±0.1nm, which corresponds to the surface coverage of 79% of its full packed monolayer. At the same time, a linear increase of film thickness with increasing number of layers was also confirmed by SPR characterizations. The data of XPS and IR-RAS show that Zr4+ ions interact with both the phosphate groups and nitrogenous bases of DNA and load into the framework of DNA. Furthermore, the interactions between this composite film and heme protein cytochrome c (Cyt c) were investigated by SPR spectroscopy and electrochemistry. Compared with the adsorption of Cyt c on DNA monolayer, this composite multilayer film can obviously enhance the amount of immobilized Cyt c confirmed by SPR reflectivity-incident angle (R-θ) curves. Cyclic voltammetry (CV) indicates the Cyt c adsorbed on the composite film is electroactive, and the enhancement of peak current in CV indirectly verifies the increase of the amount of immobilized Cyt c. [Copyright &y& Elsevier]

DNA, drug delivery, nanostructures, self-assembly, stimuli-responsive Keywords: DNA; drug delivery; nanostructures; self-assembly; stimuli-responsive EN DNA drug delivery nanostructures self-assembly stimuli-responsive 1 1 1 02/26/21 20210224 NES 210224 B Intelligent stimuli-responsive DNA b nanostructures have attracted increasing attention for biological and biomedical research owing to their promising native biocompatibility, programmability, multifunctionality, responsiveness to biological cues, and easy implementation for designing new materials. Frontispiece: Construction of Smart Stimuli-Responsive DNA Nanostructures for Biomedical Applications. [Extracted from the article]

A correction to the article "DNA Computing Circuits Using Libraries of DNAzyme Subunits" is presented.

DNAzyme-based chemiluminescence assay exhibits excellent performance in bioanalysis but their operation in acid conditions remains challengeable. Herein, we constructed an acid-improved DNAzyme-based isothermal enzyme-free concatenated DNA circuit with significantly reduced background and simultaneously improved signal-to-noise ratio for miRNA detection. The chemiluminescence miRNA assay is composed of catalyzed hairpin assembly (CHA), hybridization chain reaction (HCR), and hemin/G-quadruplex DNAzyme units. The analyte initiates the self-assembly of CHA hairpins into numerous dsDNA, which triggers the subsequent autonomous cross-opening of HCR hairpins to generate long nanowires consisting of the hemin/G-quadruplex DNAzyme. The DNAzyme catalyzes the oxidation of luminol by hydrogen peroxide for the cascaded amplified chemiluminescence signal. The acid-improved property was demonstrated to be closely associated with the low catalytic activity of aggregated hemin under acidic conditions and the remained multiple amplified signal through concatenated DNA circuit. The general DNA circuit exhibited high sensitivity for miRNA-21 detection and chemiluminescence imaging under acidic conditions with a recognition hairpin. The acid-improved DNAzyme-based concatenated DNA circuit is promising to expand the application of chemiluminescence assay and provide a valuable strategy for early diagnosis and prognosis of cancer. An acid-improved concatenated chemiluminescence DNA circuit was successfully constructed for sensitive and selective detection and imaging of miRNA with significantly reduced background and simultaneously improved signal-to-noise ratio. [Display omitted] • The acid-improved hemin/G-quadruplex DNAzyme-based concatenated DNA circuit was constructed with high signal-to-noise ratio. • The acid-improved property is demonstrated to be closely associated with the low catalytic activity of aggregated hemin. • The concatenated chemiluminescence DNA biosensor exhibits high sensitivity and selectivity for miRNA detection and imaging. [ABSTRACT FROM AUTHOR]

Polynucleotide kinase (PNK) plays a crucial role in phosphorylation-related DNA repair, while its real time tracking and monitoring is unexplored for limited sensitivity and robustness of current PNK sensing strategies in complex biological environment. Herein, we proposed a concatenated hybridization chain reaction (Con-HCR)-based PNK sensing platform for ultra-sensitive PNK assay and intracellular imaging. In the presence of PNK, the 5′-hydroxyl termini of hairpin H p was phosphorylated for λ exonuclease (λ Exo)-mediated DNA cleavage reaction. This leads to the generation of initiator I for stimulating the subsequent Con-HCR-motivated assembly of branched dsDNA nanostructures with tremendously amplified Förster resonance energy transfer (FRET) signal. Owing to the multiple-responsive recognitions of PNK/exonuclease and the dual amplification of Con-HCR, the proposed method realized the sensitive and selective PNK assay as well as the screening of PNK inhibitors. This FRET-based signal transduction provides a straightforward and accurate procedure for analyzing PNK from complex cell lysate. Furthermore, the robust feature of the present system enabled their extensive application in monitoring the varied expression levels of intracellular PNK in living cells. In view of these remarkable characters, our Con-HCR-mediated PNK sensing strategy shows more potential applications in clinical diagnosis and new drug discovery researches. A concatenated hybridization chain reaction (Con-HCR)-mediated polynucleotide kinase (PNK) sensing platform was successfully constructed for sensitively and selectively detecting PNK, for screening PNK inhibitors and for realizing intracellular PNK imaging. Image 1 • An isothermal autonomous cascaded hybridization chain reaction (Con-HCR) circuit is constructed with ultralow background. • The Con-HCR-mediated polynucleotide kinase (PNK) sensing platform exhibits high sensitivity and selectivity in cell lysates. • Our Con-HCR imaging system can track the varied expressions of intracellular PNK with high robustness and accuracy. [ABSTRACT FROM AUTHOR]