Nucleoapzymes: Hemin/G-Quadruplex DNAzyme-Aptamer Binding Site Conjugates with Superior Enzyme-like Catalytic Functions

Mobile phone-assisted imprinted nanozyme for bicolor colorimetric visual detection of erythromycin in river water and milk samples

The residues of erythromycin (ERY) may have negative impacts on the ecological environment, health, and food safety. How to detect ERY effectively and visually is a challenging issue. Herein, we synthesized a molecularly imprinted polymer based nanozymes for selective detection of erythromycin (ERY-MIPNs) at neutral pH, and developed a mobile phone-assisted bicolor colorimetric detection system. This system produced a wide range of color changes from blue to pinkish purple as the ERY concentration increased, making it easy to capture the visualization result. Also, the system showed good sensitivity to ERY ranging from 15 to 135 μM, with a detection limit of 1.78 μM. In addition, the system worked well in the detection of ERY in river water and milk, with the recoveries of 95.57% ∼ 103.20%. These data suggests that this strategy is of considerable potential for practical applications and it provides a new idea for visual detection with portable measurement.

A Cost-Effective Hemin-Based Artificial Enzyme Allows for Practical Applications

Nanomaterials excel in mimicking the structure and function of natural enzymes while being far more interesting in terms of structural stability, functional versatility, recyclability, and large-scale preparation. Herein, the story assembles hemin, histidine analogs, and G-quadruplex DNA in a catalytically competent supramolecular assembly referred to as assembly-activated hemin enzyme (AA-heminzyme). The catalytic properties of AA-heminzyme are investigated both in silico (by molecular docking and quantum chemical calculations) and in vitro (notably through a systematic comparison with its natural counterpart horseradish peroxidase, HRP). It is found that this artificial system is not only as efficient as HRP to oxidize various substrates (with a turnover number kcat of 115 s-1) but also more practically convenient (displaying better thermal stability, recoverability, and editability) and more economically viable, with a catalytic cost amounting to <10% of that of HRP. The strategic interest of AA-heminzyme is further demonstrated for both industrial wastewater remediation and biomarker detection (notably glutathione, for which the cost is decreased by 98% as compared to commercial kits).

Rapid, portable, and sensitive detection of CaMV35S by RPA-CRISPR/Cas12a-G4 colorimetric assays with high accuracy deep learning object recognition and classification

Fast, sensitive, and portable detection of genetic modification contributes to agricultural security and food safety. Here, we developed RPA-CRISPR/Cas12a-G-quadruplex colorimetric assays that can combine with intelligent recognition by deep learning algorithms to achieve sensitive, rapid, and portable detection of the CaMV35S promoter. When the crRNA-Cas12a complex recognizes the RPA amplification product, Cas12 cleaves the G-quadruplex, causing the G4-Hemin complex to lose its peroxide mimetic enzyme function and be unable to catalyze the conversion of ABTS2- to ABTS, allowing CaMV35S concentration to be determined based on ABTS absorbance. By utilizing the RPA-CRISPR/Cas12a-G4 assay, we achieved a CaMV35S limit of detection down to 10 aM and a 0.01 % genetic modification sample in 45 min. Deep learning algorithms are designed for highly accurate classification of color results. Yolov5 objective finding and Resnet classification algorithms have been trained to identify trace (0.01 %) CaMV35S more accurately than naked eye colorimetry. We also coupled deep learning algorithms with a smartphone app to achieve portable and rapid photo identification. Overall, our findings enable low cost ($0.43), high accuracy, and intelligent detection of the CaMV35S promoter.

Enhancing the substrate selectivity of enzyme mimetics in biosensing and bioassay: Novel approaches

A substantial development in nanoscale materials possessing catalytic activities comparable with natural enzymes has been accomplished. Their advantages were owing to the excellent sturdiness in an extreme environment, possibilities of their large-scale production resulting in higher profitability, and easy manipulation for modification. Despite these advantages, the main challenge for artificial enzyme mimetics is the lack of substrate selectivity where natural enzymes flourish. This review addresses this vital problem by introducing substrate selectivity strategies to three classes of artificial enzymes: molecularly imprinted polymers, nanozymes (NZs), and DNAzymes. These rationally designed strategies enhance the substrate selectivity and are discussed and exemplified throughout the review. Various functional mechanisms associated with applying enzyme mimetics in biosensing and bioassays are also given. Eventually, future directives toward enhancing the substrate selectivity of biomimetics and related challenges are discussed and evaluated based on their efficiency and convenience in biosensing and bioassays.

Ratiometric G-quadruplex/hemin DNAzymes with low-dosage associative substrates

BACKGROUND

G-quadruplex (G4)/hemin DNAzymes with conversion of substrates into colorimetric readouts are well recognized as convenient biocatalysis tools in sensor development. However, the previously developed colorimetric G4/hemin DNAzymes are diffusive substrate-based DNAzymes (DSBDs). The current colorimetric DSBDs have several drawbacks including high dosage (∼mM) of diffusive substrates (DSs), colorimetric product toxicity, and single colorimetric readout without tolerance to fluctuation of experimental factors and background. In addition, the usage of high-dosage DSs can smear the G4 foldings and their discard is more harmful to environment. Therefore, exploring alternative DNAzymes with potential to overcome these drawbacks of DSBDs is urgently needed.

RESULTS

We herein developed associative substrate-based DNAzymes (ASBDs). Cyanine dyes were selected as associative substrates (ASs) due to their binding competency with G4/hemin DNAzymes. With respect to DSBDs, ASBDs needed only low dosage (∼10 μM) of ASs to be able to cause a rapid and visible substrate conversion. In addition, since cyanine dyes are NIR dyes with high extinction coefficients and their conversion products have absorption bands at shorter wavelength. Therefore, a colorimetric ratio response can be developed to follow activities of G4/hemin DNAzymes with competency to tolerate fluctuation of experimental factors and background. In particular, herein developed ASBDs can endure somewhat concentration fluctuation of H2O2. ASBDs are able to cowork with other enzymes (for example, glucose oxidase) to realize cascade sensing.

SIGNIFICANCE

The developed ASBDs can operate at low dosage of substrates with a colorimetric ratio response and can overcome the drawbacks met in DSBDs. We expect that, by designing ASs with fruitful color panel in the future, our work will inspire more interesting in developing environment-benign and low-carbon G4/hemin DNAzymes and desired colorful high-performance sensors.

Aptamer-Modified Homogeneous Catalysts, Heterogenous Nanoparticle Catalysts, and Photocatalysts: Functional "Nucleoapzymes", "Aptananozymes", and "Photoaptazymes"

Conjugation of aptamers to homogeneous catalysts ("nucleoapzymes"), heterogeneous nanoparticle catalysts ("aptananozymes"), and photocatalysts ("photoaptazymes") yields superior catalytic/photocatalytic hybrid nanostructures emulating functions of native enzymes and photosystems. The concentration of the substrate in proximity to the catalytic sites ("molarity effect") or spatial concentration of electron-acceptor units in spatial proximity to the photosensitizers, by aptamer-ligand complexes, leads to enhanced catalytic/photocatalytic efficacies of the hybrid nanostructures. This is exemplified by sets of "nucleoapzymes" composed of aptamers conjugated to the hemin/G-quadruplex DNAzymes or metal-ligand complexes as catalysts, catalyzing the oxidation of dopamine to aminochrome, oxygen-insertion into the Ar─H moiety of tyrosinamide and the subsequent oxidation of the catechol product into aminochrome, or the hydrolysis of esters or ATP. Also, aptananozymes consisting of aptamers conjugated to Cu2+ - or Ce4+ -ion-modified C-dots or polyadenine-stabilized Au nanoparticles acting as catalysts oxidizing dopamine or operating bioreactor biocatalytic cascades, are demonstrated. In addition, aptamers conjugated to the Ru(II)-tris-bipyridine photosensitizer or the Zn(II) protoporphyrin IX photosensitizer provide supramolecular photoaptazyme assemblies emulating native photosynthetic reaction centers. Effective photoinduced electron transfer followed by the catalyzed synthesis of NADPH or the evolution of H2 is demonstrated by the photosystems. Structure-function relationships dictate the catalytic and photocatalytic efficacies of the systems.

Biosystem-Inspired Engineering of Nanozymes for Biomedical Applications

Nanozymes with intrinsic enzyme-mimicking activities have shown great potential to become surrogates of natural enzymes in many fields by virtue of their advantages of high catalytic stability, ease of functionalization, and low cost. However, due to the lack of predictable descriptors, most of the nanozymes reported in the past have been obtained mainly through trial-and-error strategies, and the catalytic efficacy, substrate specificity, as well as practical application effect under physiological conditions, are far inferior to that of natural enzymes. To optimize the catalytic efficacies and functions of nanozymes in biomedical settings, recent studies have introduced biosystem-inspired strategies into nanozyme design. In this review, recent advances in the engineering of biosystem-inspired nanozymes by leveraging the refined catalytic structure of natural enzymes, simulating the behavior changes of natural enzymes in the catalytic process, and mimicking the specific biological processes or living organisms, are introduced. Furthermore, the currently involved biomedical applications of biosystem-inspired nanozymes are summarized. More importantly, the current opportunities and challenges of the design and application of biosystem-inspired nanozymes are discussed. It is hoped that the studies of nanozymes based on bioinspired strategies will be beneficial for constructing the new generation of nanozymes and broadening their biomedical applications.

Advances in colorimetric biosensors of exosomes: novel approaches based on natural enzymes and nanozymes

Exosomes are 30-150 nm vesicles derived from diverse cell types, serving as one of the most important biomarkers for early diagnosis and prognosis of diseases. However, the conventional detection method for exosomes faces significant challenges, such as unsatisfactory sensitivity, complicated operation, and the requirement of complicated devices. In recent years, colorimetric exosome biosensors with a visual readout underwent rapid development due to the advances in natural enzyme-based assays and the integration of various types of nanozymes. These synthetic nanomaterials show unique physiochemical properties and catalytic abilities, enabling the construction of exosome colorimetric biosensors with novel principles. This review will illustrate the reaction mechanisms and properties of natural enzymes and nanozymes, followed by a detailed introduction of the recent advances in both types of enzyme-based colorimetric biosensors. A comparison between natural enzymes and nanozymes is made to provide insights into the research that improves the sensitivity and convenience of assays. Finally, the advantages, challenges, and future directions of enzymes as well as exosome colorimetric biosensors are highlighted, aiming at improving the overall performance from different approaches.

A smartphone-assisted one-step bicolor colorimetric detection of glucose in neutral environment based on molecularly imprinted polymer nanozymes

In order to improve the specificity and the peroxidase-like activity of nanozyme at the neutral pH as well as to facilitate the naked-eye visual detection of the analyte concentration, a nanozyme based on molecularly imprinted polymers (MIPNs) for selective and bicolor colorimetric detection of glucose in neutral environment was developed. Compared with free nanozyme, the synthesized MIPNs showed a better catalytic capability, with a catalytic efficiency (kcat/Km) 9.5 times higher than that of free nanozyme. The kinetics experiment showed that the MIPNs demonstrated a fast kinetic feature and the kinetic data fitted a pseudo-first-order model. In practical application, the color of the detection system changed gradually from pink to blue as the glucose concentration increased in a broad linear range from 0 to 3 mM, with a detection limit of 6.22 μM. The colorimetric visualization of glucose concentration was read with a smartphone and no other instrument was needed. Therefore, a manageable and highly efficient method for the MIPNs-catalyzed visualization at the neutral pH and the one-step bicolor visual detection was constructed. This newly established method may also provide a new idea for further development and application of nanozymes.

Bioorthogonal Chemistry in Translational Research: Advances and Opportunities

Bioorthogonal chemistry is a rapidly expanding field of research that involves the use of small molecules that can react selectively with biomolecules in living cells and organisms, without causing any harm or interference with native biochemical processes. It has made significant contributions to the field of biology and medicine by enabling selective labeling, imaging, drug targeting, and manipulation of bio-macromolecules in living systems. This approach offers numerous advantages over traditional chemistry-based methods, including high specificity, compatibility with biological systems, and minimal interference with biological processes. In this review, we provide an overview of the recent advancements in bioorthogonal chemistry and their current and potential applications in translational research. We present an update on this innovative chemical approach that has been utilized in cells and living systems during the last five years for biomedical applications. We also highlight the nucleic acid-templated synthesis of small molecules by using bioorthogonal chemistry. Overall, bioorthogonal chemistry provides a powerful toolset for studying and manipulating complex biological systems, and holds great potential for advancing translational research.

A DNA Origami-based Bactericide for Efficient Healing of Infected Wounds

Bacteria infection is a significant obstacle in the clinical treatment of exposed wounds facing widespread pathogens. Herein, we report a DNA origami-based bactericide for efficient anti-infection therapy of infected wounds in vivo. In our design, abundant DNAzymes (G4/hemin) can be precisely organized on the DNA origami for controllable generation of reactive oxygen species (ROS) to break bacterial membranes. After the destruction of the membrane, broad-spectrum antibiotic levofloxacin (LEV, loaded in the DNA origami through interaction with DNA duplex) can be easily delivered into the bacteria for successful sterilization. With the incorporation of DNA aptamer targeting bacterial peptidoglycan, the DNA origami-based bactericide can achieve targeted and combined antibacterial therapy for efficiently promoting the healing of infected wounds. This tailored DNA origami-based nanoplatform provides a new strategy for the treatment of infectious diseases in vivo.

Supramolecular Polyaniline-Metal Ion as Chiral Nanozymes for Enantioselective Catalysis

Understanding origin of asymmetric information encoded on chiral nanozymes is important in mediating enantioselective catalysis. Herein, the supramolecular chiral nanozymes constructed from P/M-polyaniline (P/M-PANI) nanotwists and metal ions (M2+ , M = Cu, Ni, Co, and Zn) are designed through thioglycolic acid (TA) without chiral molecules to show the regulated catalytic efficiency and enantioselectivity. With combination of chiral environment from supramolecular scaffolds and catalytic center from metal ions, the P-PANI-TA-M2+ as nanozymes show preference to 3,4-dihydroxy-S-phenylalanine (S-DOPA) oxidation while the M-PANI-TA-M2+ show better selectivity to R-DOPA oxidation. Among them, though the Cu2+ doped supramolecular nanotwists show the highest catalytic efficiency, the Co2+ doped ones with moderate catalytic efficiency can exhibit the best enantioselectivity with select factor as high as 2.07. The molecular dynamic (MD) simulation clarifies the mechanism of enantioselective catalysis caused by the differential kinetics with S/R-DOPA enantiomers adsorbed on chiral PANI surface and free in solution. This work systematically studies the synergistic effect between the chiral supramolecular nanostructures assembled by achiral species and metal ions as peroxidase-like catalytic centers to regulate the enantioselectivity, providing deep understanding of the origin of asymmetric catalysis and serving as strong foundation to guide the design of nanozymes with high enantioselectivity.

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

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

Selection of allosteric dnazymes that can sense phenylalanine by expression-SELEX

Aptamers are ligand-binding RNA or DNA molecules and have been widely examined as biosensors, diagnostic tools, and therapeutic agents. The application of aptamers as biosensors commonly requires an expression platform to produce a signal to report the aptamer-ligand binding event. Traditionally, aptamer selection and expression platform integration are two independent steps and the aptamer selection requires the immobilization of either the aptamer or the ligand. These drawbacks can be easily overcome through the selection of allosteric DNAzymes (aptazymes). Herein, we used the technique of Expression-SELEX developed in our laboratory to select for aptazymes that can be specifically activated by low concentrations of l-phenylalanine. We chose a previous DNA-cleaving DNAzyme known as II-R1 as the expression platform for its low cleavage rate and used stringent selection conditions to drive the selection of high-performance aptazyme candidates. Three aptazymes were chosen for detailed characterization and these DNAzymes were found to exhibit a dissociation constant for l-phenylalanine as low as 4.8 μM, a catalytic rate constant improvement as high as 20 000-fold in the presence of l-phenylalanine, and the ability to discriminate against closely related l-phenylalanine analogs including d-phenylalanine. This work has established the Expression-SELEX as an effective SELEX method to enrich high-quality ligand-responsive aptazymes.

A label-free colorimetric 3D paper-based device for ochratoxin A detection using G-quadruplex/hemin DNAzyme with a smartphone readout

The colorimetric sensor usually depends on enzyme-mediated signal amplification to achieve trace analysis of ochratoxin A (OTA) residues in food samples. However, the enzyme labeling and manual addition of reagents steps increased assay time and operation complexity, restricting their application in point-of-care testing (POCT). Herein, we report a label-free colorimetric device integrating a 3D paper-based analytical device and a smartphone as handheld readout for rapid and sensitive detection of OTA. Using vertical-flow design, the paper-based analytical device enables the specific recognition of target and self-assembly of G-quadruplex (G4)/hemin DNAzyme to be performed, then employs DNAzyme for transducing the OTA binding event signal into a colorimetric signal. The design of independent functional units, including biorecognition unit, self-assembly unit and colorimetric units, which can address crowding and disorder of biosensing interfaces and improve the recognition efficiency of aptamer (apta). In addition, we eliminated signal losses and nonuniform coloring by introducing carboxymethyl chitosan (CMCS) to obtain perfectly focused signals on colorimetric unit. On the basis of parameter optimization, the device exhibited a detection range of 0.1-500 ng/mL and a detection limit of 41.9 pg/mL for OTA. Importantly, good results were obtained in spiked real samples, indicating applicability and reliability of developed device.

RNA extraction-free workflow integrated with a single-tube CRISPR-Cas-based colorimetric assay for rapid SARS-CoV-2 detection in different environmental matrices

On-site environmental surveillance of viruses is increasingly important for infection prevention and pandemic control. Herein, we report a facile single-tube colorimetric assay for detecting severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from environmental compartments. Using glycerol as the phase separation additive, reverse transcription recombinase polymerase amplification (RT-RPA), CRISPR-Cas system activation, G-quadruplex (G4) cleavage, and G4-based colorimetric reaction were performed in a single tube. To further simplify the test, viral RNA genomes used for the one-tube assay were obtained via acid/base treatment without further purification. The whole assay from sampling to visual readout was completed within 30 min at a constant temperature without the need for sophisticated instruments. Coupling the RT-RPA to CRISPR-Cas improved the reliability by avoiding false positive results. Non-labeled cost-effective G4-based colorimetric systems are highly sensitive to CRISPR-Cas cleavage events, and the proposed assay reached the limit of detection of 0.84 copies/µL. Moreover, environmental samples from contaminated surfaces and wastewater were analyzed using this facile colorimetric assay. Given its simplicity, sensitivity, specificity, and cost-effectiveness, our proposed colorimetric assay is highly promising for applications in on-site environmental surveillance of viruses.

Heme-Dependent Supramolecular Nanocatalysts: A Review

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

A universal approach for synthesis of copper nanoclusters templated by G-rich oligonucleotide sequences and their applications in sensing

Herein, five common G4 sequences have been selected, including three different length of telomere DNA, hemin aptamer, and thrombin aptamer, to synthesize Cu nanoclusters (Cu NCs) in-situ. All G4s are proper templates for Cu NCs with low temperature treatment. The particles (G4-Cu NCs) smaller than 3 nm in diameter were obtained and showed light green fluorescence. This is the first report of metal clusters templated by G4s in-situ. As proof of the concept, hemin and alkaline phosphatase (ALP) were used as the targets to test whether the system can monitor the interaction between G4s and its substrate. The results suggest that G4-Cu NCs can indicate the behavior of G4 and its interaction with hemin, and sensing ALP is achieved with the aid of ATP. The linear ranges of hemin and ALP are 300-4000 nM and 10-500 U/L, respectively, and the corresponding limits of detection as low as 97 nM for hemin and 2.8 U/L for ALP. Moreover, this present system has been successfully applied for the detection of ALP in human serum samples with satisfactory recoveries. This synthesis approach is universal, and it can be easily extended to evaluating the formation of G4, or monitoring the interaction between G4 and its substrate, or selective targeting individual G4, or sensitive detection of other important biomarkers by changing template G4 sequence.

Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase

Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number k_cat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.

A Novel and Label-Free Chemiluminescence Detection of Zearalenone Based on a Truncated Aptamer Conjugated with a G-Quadruplex DNAzyme

Zearalenone (ZEN), one of the most frequently occurring mycotoxin contaminants in foods and feeds, poses considerable threat to human and animal health, owing to its acute and chronic toxicities. Thus, rapid and accurate detection of ZEN has attracted broad research interest. In this work, a novel and label-free chemiluminescence aptasensor based on a ZEN aptamer and a G-quadruplex DNAzyme was constructed. It was established on a competitive assay between ZEN and an auxiliary DNA for the aptamer, leading to activation of the G-quadruplex/hemin DNAzyme and subsequent signal amplification by chemiluminescence generation after substrate addition. To maximize the detection sensitivity, numerous key parameters including truncated aptamers were optimized with molecular docking analysis. Upon optimization, our aptasensor exhibited a perfect linear relationship (R² = 0.9996) for ZEN detection in a concentration range of 1-100 ng/mL (3.14-314.10 nM) within 40 min, achieving a detection limit of 2.85 ng/mL (8.95 nM), which was a 6.7-fold improvement over that before optimization. Most importantly, the aptasensor obtained a satisfactory recovery rate of 92.84-137.27% and 84.90-124.24% for ZEN-spiked wheat and maize samples, respectively. Overall, our label-free chemiluminescence aptasensor displayed simplicity, sensitivity, specificity and practicality in real samples, indicating high application prospects in the food supply chain for rapid detection of ZEN.

Preparation and Application of Nanozymes with Uricase-Like Activity Based on Molecularly Imprinted Polymers

Nanozymes have advantages over natural enzymes in terms of efficiency, stability, and economy. MVSM (Mixed Valence State MOF) is a nano-oxidase with uricase-like activity that may catalyze uric acid (UA) in the body into allantoin and H₂ O₂ to treat gout and hyperuricemia by substituting natural uricase. However, it cannot specifically identify and choose UA. To increase the selectivity and affinity of MVSM for UA, the composite material MVSM@MIP is innovatively synthesized using a new synthetic approach termed the "two-step synthesis method," which may prevent UA from being oxidized by MVSM during manufacture in this study. At the same time, this study also provides experimental proof of the effective creation of the material, the advantages of the "two-step synthesis approach," and the high selectivity and affinity of MVSM@MIP for UA. Based on these findings, the suggested technique may be used to effectively catalyze uric acid in human urine with high activity.

Aptamer-Modified Au Nanoparticles: Functional Nanozyme Bioreactors for Cascaded Catalysis and Catalysts for Chemodynamic Treatment of Cancer Cells

Polyadenine-stabilized Au nanoparticles (pA-AuNPs) reveal dual nanozyme catalytic activities toward the H₂O₂-mediated oxidation of dopamine to aminochrome and toward the aerobic oxidation of glucose to gluconic acid and H₂O₂. The conjugation of a dopamine-binding aptamer (DBA) to the pA-AuNPs yields aptananozyme structures catalyzing simultaneously the H₂O₂-mediated oxidation of dopamine to aminochrome through the aerobic oxidation of glucose. A set of aptananozymes consisting of DBA conjugated through the 5'- or 3'-end directly or spacer bridges to pA-AuNPs were synthesized. The set of aptananozymes revealed enhanced catalytic activities toward the H₂O₂-catalyzed oxidation of dopamine to dopachrome, as compared to the separated pA-AuNPs and DBA constituents, and structure-function relationships within the series of aptananozymes were demonstrated. The enhanced catalytic function of the aptananozymes was attributed to the concentration of the dopamine at the catalytic interfaces by means of aptamer-dopamine complexes. The dual catalytic activities of aptananozymes were further applied to design bioreactors catalyzing the effective aerobic oxidation of dopamine in the presence of glucose. Mechanistic studies demonstrated that the aptananozymes generate reactive oxygen species. Accordingly, the AS1411 aptamer, recognizing the nucleolin receptor associated with cancer cells, was conjugated to the pA-AuNPs, yielding a nanozyme for the chemodynamic treatment of cancer cells. The AS1411 aptamer targets the aptananozyme to the cancer cells and facilitates the selective permeation of the nanozyme into the cells. Selective cytotoxicity toward MDA-MB-231 breast cancer cells (ca. 70% cell death) as compared to MCF-10A epithelial cells (ca. 2% cell death) is demonstrated.

Aptamer-Protein Structures Guide In Silico and Experimental Discovery of Aptamer-Short Peptide Recognition Complexes or Aptamer-Amino Acid Cluster Complexes

A method to computationally and experimentally identify aptamers against short peptides or amino acid clusters is introduced. The method involves the selection of a well-defined protein aptamer complex and the extraction of the peptide sequence participating in the binding of the protein to the aptamer. The subsequent fragmentation of the peptide sequence into short peptides and the in silico docking-guided identification of affinity complexes between the miniaturized peptides and the antiprotein aptamer, followed by experimental validation of the binding features of the short peptides with the antiprotein aptamers, leads to the identification of new short peptide-aptamer complexes. This is exemplified with the identification of the pentapeptide RYERN as the scaffold that binds thrombin to the DNA thrombin aptamer (DNA TA). In silico docking studies followed by microscale thermophoresis (MST) experiments demonstrate that the miniaturized tripeptides RYE, YER, and ERN reveal selective binding affinities toward the DNA TA. In addition, docking and MST experiments show that the ribonucleotide-translated RNA TA shows related binding affinities of YER to the DNA TA. Most importantly, we demonstrate that the separated amino acids Y/E/R assemble as a three amino acid cluster on the DNA TA and RNA TA aptamers in spatial configurations similar to the tripeptide YER on the respective aptamers. The clustering phenomenon is selective for the YER tripeptide system. The method to identify binding affinities of miniaturized peptides to known antiprotein aptamers and the specific clustering of single amino acids on the aptamers is further demonstrated by in silico and experimental identification of the binding of the tripeptide RET and the selective clustering of the separated amino acids R/E/T onto a derivative of the AS1411 aptamer against the nucleolin receptor protein.

Modulation of Enzyme Cascade Activity by Local Substrate Enrichment and Exclusion on DNA Nanostructures

Substrate confinement and channeling play a critical role in multienzyme pathways and are considered to impact the catalytic efficiency and specificity of biomimetic and artificial nanoreactors. Here we reported a modulation of a multienzyme system with the cascade activity impacted by the surface affinity binding to substrate molecules. A DNA origami modified with aptamers was used to bind and enrich ATP molecules in the local area of immobilized enzymes, thereby enhancing the activity of an enzyme cascade by more than 2-fold. Alternatively, DNA nanostructure modified with blocked aptamers does not bind with ATP, thereby reducing the activity of the enzyme cascade. The Michaelis-Menten kinetics showed decreased apparent K_M values (∼3-fold lower) for enzyme nanostructures modified with aptamers, suggesting the higher effective substrate concentration near enzymes due to the local enrichment of substrates. Conversely, increased apparent K_M values (∼2-fold higher) were observed for enzyme nanostructures modified with blocked aptamers, possibly due to the exclusion of substrates approaching the surface. The similar concept of this modified surface-substrate interaction should be applicable to other multienzyme systems immobilized on nanostructures, which could be useful in the development of biomimetic nanoreactors.

Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State

RNA aptamers are single-stranded oligonucleotides that bind to specific molecular targets with high affinity and specificity. To design aptamers for new applications, it is critical to understand the ligand binding mechanism in terms of the structure and dynamics of the ligand-bound and apo states. The problem is that most of the NMR or X-ray crystal structures available for RNA aptamers are for ligand-bound states. Available apo state structures, mostly characterized by crystallization under nonphysiological conditions or probed by low resolution techniques, might fail to represent the diverse structural variations of the apo state in solution. Here, we develop an approach to obtain a representative ensemble of apo structures that are based on in silico RNA 3D structure prediction and in vitro experiments that characterize base stacking. Using the neomycin-B aptamer as a case study, an ensemble of structures for the aptamer in the apo (unbound) state are validated and then used to investigate the ligand-binding mechanism for the aptamer in complex with neomycin-B.

Switchable and dynamic G-quadruplexes and their applications

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

Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures

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

Cascaded dissipative DNAzyme-driven layered networks guide transient replication of coded-strands as gene models

Dynamic, transient, out-of-equilibrium networks guide cellular genetic, metabolic or signaling processes. Designing synthetic networks emulating natural processes imposes important challenges including the ordered connectivity of transient reaction modules, engineering of the appropriate balance between production and depletion of reaction constituents, and coupling of the reaction modules with emerging chemical functions dictated by the networks. Here we introduce the assembly of three coupled reaction modules executing a cascaded dynamic process leading to the transient formation and depletion of three different Mg²⁺-ion-dependent DNAzymes. The transient operation of the DNAzyme in one layer triggers the dynamic activation of the DNAzyme in the subsequent layer, leading to a three-layer transient catalytic cascade. The kinetics of the transient cascade is computationally simulated. The cascaded network is coupled to a polymerization/nicking DNA machinery guiding transient synthesis of three coded strands acting as “gene models”, and to the rolling circle polymerization machinery leading to the transient synthesis of fluorescent Zn(II)-PPIX/G-quadruplex chains or hemin/G-quadruplex catalytic wires.

A reaction network executing a cascaded transient formation and depletion of three different catalytic strands is introduced. The system is coupled to the secondary temporal synthesis of different coded strands as gene models.

Inactivation Kinetics of G‐Quadruplex/Hemin Complex and Optimization for More Reliable Catalysis

Reliable catalysis is critical for the synthesis of various chemicals, molecular sensing and biomedicine. G-quadruplex/Hemin (GQH) complex, a peroxidase-mimicking DNAzyme, has been widely used in various publications. However, a concern exists about the unstable kinetics of GQH-catalyzed peroxidation. This work investigates several factors that result in the inactivation of GQH and the signal degradation during long reaction periods, including pH, buffer component, the selection of substrate and the oxidation damage of cofactor. Using colorimetric and fluorescent assays, GQH was found to be highly unstable under basic conditions with 50 % of GQH activity lost within 2 minutes at high H₂ O₂ concentrations. Appropriate conditions and substrates are suggested for accurately characterizing GQH-catalyzed reactions, as well as optimization to improve the catalytic reliability, such as the use of polyhistidine and cascade reactions. These results could be useful for GQH-related applications.

Visible light-driven i-motif-based DNAzymes

DNA foldings provide variant possibilities to develop DNAzymes with remarkable catalytic performance. In spite of fruitful reports on G-quadruplex DNAzymes, four-stranded cytosine-rich i-motifs have not been explored as the potential skeletons of DNAzymes. In this work, we developed a visible light-driven DNAzyme based on human telomeric i-motifs using a natural photosensitizer of hypericin (Hyp) as the cofactor and dissolved oxygen as the oxidant source. The i-motif folding in acidic solution caused the distal thymine overhangs at the 3' and 5' ends to approach each other to provide a favorable binding site for Hyp via an interaction of fully complementary hydrogen bonding. However, the i-motifs without the distal overhangs or with the inappropriate overhang length and the base identity exhibited no binding with Hyp. The binding event converted Hyp from the fully dark state to the emissive state under visible light illumination. Subsequently, the excited Hyp had an opportunity to transfer energy to dissolved oxygen. Resultantly, singlet oxygen (¹O₂) was generated to initiate the substrate oxidation. The catalytic performance of the DNAzyme can be improved using a long-lived mediator. Our developed i-motif-based DNAzyme can be driven by almost the whole range of visible lights, suggesting broad applications in the photocatalytic fields, for example, as an alternative strategy in developing biodevices.

Systems chemistry of peptide-assemblies for biochemical transformations

During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.

DNAzyme-controlled plasmonic coupling for SERS-based determination of Salmonella typhimurium using hybridization chain reaction self-assembled G-quadruplex

A facile and rapid SERS strategy for S. typhimurium detection based on hybridization chain reaction (HCR) self-assembled G-quadruplex DNAzyme (GQH DNAzyme)-controlled plasmonic coupling was developed. GQH DNAzyme is introduced as a biocatalyst to catalyze the oxidation of L-cysteines to cysteines (thiols to disulfides) to assist SERS signal transduction. This is the first time that the self-assembled split GQH DNAzyme-controlled plasmonic coupling is integrated with SERS sensing. The results reveal the proposed SERS strategy can quantify S. typhimurium with a wide linear range (5 to 10⁵ cfu mL^-1) and a low detection limit (4 cfu mL^-1; n = 5, mean ± standard deviation) and RSD of 7%. The method exhibited preeminent detection performance in spiked samples with recoveries of 93.1-117%. The proposed strategy has great potential for being a versatile SERS platform for detecting a wide spectrum of analytes by replacing them with the corresponding recognition elements. Therefore, this study not only creates a practical platform for pathogenic bacteria identification and related food safety testing and environmental monitoring, but also provides a new paradigm for building SERS sensor. A facile and rapid SERS strategy for S. Typhimurium detection based on hybridization chain reaction (HCR) self-assembled G-quadruplex DNAzyme-controlled plasmonic coupling.

Enzyme-Loaded Hemin/G-Quadruplex-Modified ZIF-90 Metal-Organic Framework Nanoparticles: Bioreactor Nanozymes for the Cascaded Oxidation of N-hydroxy-l-arginine and Sensing Applications

Biocatalytic cascades are challenging to operate in homogeneous solution, where diffusional mass transport hinders efficient communication between the reactive components. There is great interest in developing devices to perform such transformations in confined environments, which increase the efficiency of the cascaded process by generating high local concentrations of the reactive species. Herein, a bioreactor-nanozyme assembly is introduced for the cascaded aerobic oxidation of N-hydroxy-l-arginine (NOHA) to citrulline in the presence of glucose. The reaction mimics a key step in the nitric oxide synthase oxidation of l-arginine in nature. The system consists of glucose oxidase (GOx)-loaded hemin/G-quadruplex (hemin/G4)-modified ZIF-90 metal-organic framework nanoparticles. The aerobic oxidation of glucose by GOx yields H₂ O₂ that fuels the hemin/G4-catalyzed oxidation of NOHA into citrulline. The process driven by the bioreactor-nanozyme system is ≈sixfold enhanced compared to the homogeneous mixture of the biocatalysts, due to its operation in the confined environment of the nanoparticles. Extension to a three-step cascade is then demonstrated using a bioreactor composed of β-galactosidase/GOx-loaded hemin/G4-modified ZIF-90 nanoparticles activating the cascaded oxidation of NOHA to citrulline, in the presence of lactose. Moreover, the bioreactor-nanozyme hybrid is applied as a functional optical sensor of glucose, using fluorescence or chemiluminescence as readout signals.

Pillar[5]arene-Based Fluorescent Sensor Array for Biosensing of Intracellular Multi-neurotransmitters through Host-Guest Recognitions

Neurotransmitters are very important for neuron events and brain diseases. However, effective probes for analyzing specific neurotransmitters are currently lacking. Herein, we design and create a supramolecular fluorescent probe (CN-DFP5) by synthesizing a dual-functionalized fluorescent pillar[5]arene derivative with borate naphthalene and aldehyde coumarin recognition groups to identify large-scale neurotransmitters. The developed probe can detect seven model neurotransmitters by generating different fluorescence patterns through three types of host-guest interactions. The obtained signals are statistically processed by principal component analysis, thus the high-throughput analysis of neurotransmitters is realized under dual-channel fluorescence responses. The present probe combines the advantages of small-molecule-based probes to easily enter into living neurons and cross-reactive sensor arrays. Thus, the selective binding enables this probe to identify specific neurotransmitters in biofluids, living neurons, and tissues. High selectivity and sensitivity further demonstrate that the molecular device could extend to more applications to detect and image neurotransmitters.

Self-Adaptive Single-Atom Catalyst Boosting Selective Ferroptosis in Tumor Cells

Ferroptosis, resulting from the catastrophic accumulation of lipid reactive oxygen species (ROS) and the inactivation of glutathione (GSH)-dependent peroxidase 4 (GPX4), has emerged as a form of regulated cell death for cancer therapy. Despite progress made with current ferroptosis inducers, efficient systems to trigger ferroptosis remain challenging, owing largely to their low activity, uncontrollable behavior, and even nonselective interactions. Here, we report a self-adaptive ferroptosis platform by engineering a DNA modulator onto the surface of single-atom nanozymes (SAzymes). The modulator could not only specifically intensify the ROS-generating activity but also endow the SAzymes with on-demand GSH-consuming ability in tumor cells, accelerating selective and safe ferroptosis. The self-adaptive antitumor response has been demonstrated in colon cancer and breast cancer, promoting the development of selective cancer therapy.

Photoresponsive DNA materials and their applications

Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.

A DNAzyme-augmented bioorthogonal catalysis system for synergistic cancer therapy

As one of the representative bioorthogonal reactions, the copper-catalyzed click reaction provides a promising approach for in situ prodrug activation in cancer treatment. To solve the issue of inherent toxicity of Cu(i), biocompatible heterogeneous copper nanoparticles (CuNPs) were developed for the Cu-catalyzed azide–alkyne cycloaddition (CuAAC) reaction. However, the unsatisfactory catalytic activity and off-target effect still hindered their application in biological systems. Herein, we constructed a DNAzyme-augmented and targeted bioorthogonal catalyst for synergistic cancer therapy. The system could present specificity to cancer cells and promote the generation of Cu(i) via DNAzyme-induced value state conversion of DNA-templated ultrasmall CuNPs upon exposure to endogenous H₂O₂, thereby leading to high catalytic activity for in situ drug synthesis. Meanwhile, DNAzyme could produce radical species to damage cancer cells. The synergy of in situ drug synthesis and chemodynamic therapy exhibited excellent anti-cancer effects and minimal side effects. The study offers a simple and novel avenue to develop highly efficient and safe bioorthogonal catalysts for biological applications.

A DNAzyme-augmented and tumor-targeted bioorthogonal catalysis system is constructed for synergistic cancer therapy. It promotes the generation of Cu(i) and ROS using endogenous H₂O₂, thereby achieving in situ drug synthesis and chemodynamic therapy.

Visual detection of aflatoxin B1 and zearalenone via activating a new catalytic reaction of “naked” DNAzyme

It was found for the first time that the catalytic activity of “naked” DNAzyme can be modulated by aflatoxins and zearalenone to generate different color changes, which could be applied to the visual detection for the above two analytes.

Selective and Nongenetic Peroxidase Tag of Membrane Protein: a Nucleic Acid Tool for Proximity Labeling

The protein nanoenvironment on the plasma membrane is intimately linked to cellular biological functions. Elucidation of the protein nanoenvironment contributes to understanding the pathological mechanism and discovery of disease biomarkers. However, methods enabling characterization of the protein nanoenvironment in the endogenous biological environment have been rarely developed. Toward this end, we created a nucleic acid tool called Apt-Gq/h for proximity labeling to decipher the endogenous protein nanoenvironment. Here, the aptamer acts as an anchor for binding the protein of interest (POI). The G-quadruplex/hemin complex induces proximity labeling of POI via catalyzing the conversion of inert small-molecule substrates into short-lived reactive species. The labeled proteins enable the subsequent affinity-based enrichment and proteomic analysis. We first characterized Apt-Gq/h-mediated POI labeling in vitro and tested its utility by interrogating the protein nanoenvironment of POI in living cells. Taking advantage of the nongenetic, multiple reaction sites, and rapid proximity labeling, Apt-Gq/h was further utilized to imaging the cell-cell connection and amplification detection of biomarkers in living cells and tissue sections. We believe that Apt-Gq/h will be a potential tool for basic science and clinical applications.

DNA-Scaffolded Synergistic Catalysis

We report DNA-scaffolded synergistic catalysis, a concept that combines the diverse reaction scope of synergistic catalysis with the ability of DNA to precisely preorganize abiotic groups and undergo stimuli-triggered conformational changes. As an initial demonstration of this concept, we focus on Cu-TEMPO-catalyzed aerobic alcohol oxidation, using DNA as a scaffold to hold a copper cocatalyst and an organic radical cocatalyst (TEMPO) in proximity. The DNA-scaffolded catalyst maintained a high turnover number upon dilution and exhibited 190-fold improvement in catalyst turnover number relative to the unscaffolded cocatalysts. By incorporating the cocatalysts into a DNA hairpin-containing scaffold, we demonstrate that the rate of the synergistic catalytic reaction can be controlled through a reversible DNA conformational change that alters the distance between the cocatalysts. This work demonstrates the compatibility of synergistic catalytic reactions with DNA scaffolding, opening future avenues in reaction discovery, sensing, responsive materials, and chemical biology.

Photoswitchable single-stranded DNA-peptide coacervate formation as a dynamic system for reaction control

In cells, segregation allows for diverse biochemical reactions to take place simultaneously. Such intricate regulation of cellular processes is achieved through the dynamic formation and disassembly of membraneless organelles via liquid-liquid phase separation (LLPS). Herein, we demonstrate the light-controlled formation and disassembly of liquid droplets formed from a complex of polylysine (pLys) and arylazopyrazole (AAP)-conjugated single-stranded DNA. Photoswitchablility of droplet formation was also shown to be applicable to the control of chemical reactions; imine formation and a DNAzyme-catalyzed oxidation reaction were accelerated in the presence of droplets. These outcomes were reversed upon droplet disassembly. Our results demonstrate that the photoswitchable droplet formation system is a versatile model for the regulation of reactions through dynamic LLPS.

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Incorporating AAP enabled light-controlled droplet formation with ssDNA and pLys

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Droplets were reversibly formed or disassembled without altering sample composition

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Photoswitchability depended on sequence and ionic interactions but not flexibility

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Photoswitchable droplet formation accelerated uncatalyzed and catalyzed reactions

DNA-assisted site-selective protein modification

Protein modification is important for various types of biomedical research, including proteomics and therapeutics. Many methodologies for protein modification exist, but not all possess the required level of efficiency and site selectivity. This review focuses on the use of DNA to achieve the desired conversions and levels of accuracy in protein modification by using DNA (i) as a template to help concentrate dilute reactants, (ii) as a guidance system to achieve selectivity by binding specific proteins, and (iii) even as catalytic entity or construct to enhance protein modification reactions.

Bioinspired Artificial Photosynthetic Systems

Mimicking photosynthesis using artificial systems, as a means for solar energy conversion and green fuel generation, is one of the holy grails of modern science. This perspective presents recent advances towards developing artificial photosynthetic systems. In one approach, native photosystems are interfaced with electrodes to yield photobioelectrochemical cells that transform light energy into electrical power. This is exemplified by interfacing photosystem I (PSI) and photosystem II (PSII) as an electrically contacted assembly mimicking the native Z-scheme, and by the assembly of an electrically wired PSI/glucose oxidase biocatalytic conjugate on an electrode support. Illumination of the functionalized electrodes led to light-induced generation of electrical power, or to the generation of photocurrents using glucose as the fuel. The second approach introduces supramolecular photosensitizer nucleic acid/electron acceptor complexes as functional modules for effective photoinduced electron transfer stimulating the subsequent biocatalyzed generation of NADPH or the Pt-nanoparticle-catalyzed evolution of molecular hydrogen. Application of the DNA machineries for scaling-up the photosystems is demonstrated. A third approach presents the integration of artificial photosynthetic modules into dynamic nucleic acid networks undergoing reversible reconfiguration or dissipative transient operation in the presence of auxiliary triggers. Control over photoinduced electron transfer reactions and photosynthetic transformations by means of the dynamic networks is demonstrated.

DNAzyme-Functionalized Nanomaterials: Recent Preparation, Current Applications, and Future Challenges

DNAzyme-nanomaterial bioconjugates are a popular hybrid and have received major attention for diverse biomedical applications, such as bioimaging, biosensor development, cancer therapy, and drug delivery. Therefore, significant efforts are made to develop different strategies for the preparation of inorganic and organic nanoparticles (NPs) with specific morphologies and properties. DNAzymes functionalized with metal-organic frameworks (MOFs), gold nanoparticles (AuNPs), graphene oxide (GO), and molybdenum disulfide (MoS₂ ) are introduced and summarized in detail in this review. Moreover, the focus is on representative examples of applications of DNAzyme-nanomaterials over recent years, especially in bioimaging, biosensing, phototherapy, and stimulation response delivery in living systems, with their several advantages and drawbacks. Finally, the perspective regarding the future directions of research addressing these challenges is also discussed and highlighted.

Rational Utilization of Photoelectrochemistry of Photosystem II for Self-Powered Photocathodic Detection of MicroRNA in Cells

The photoanode, photosystem II (PSII)/hierarchical inverse opal (IO) TiO₂, is coupled to the complementary photocathode, PbS quantum dots (QDs)/DNA probes, which is then integrated into a two-compartment photoelectrochemical (PEC) cell to achieve a self-powered system to enable photocathodic detection of microRNA-10b from HeLa cells. In such a system, all of the PSII catalytic products, i.e., electrons, protons, and O₂, were rationally utilized and could overcome the general issue of varied O₂ levels in photocathodic detection. The correlation between the target-triggered formation of the DNA complexes and the catalytic reduction of the dissolved O₂ makes possible the steady microRNA-10b detection with good sensitivity and selectivity. This work has unveiled the ability of PSII to construct self-powered detecting devices and shed light on its application in new arenas.

Template-Regulated Bimetallic Sulfide Nanozymes with High Specificity and Activity for Visual Colorimetric Detection of Cellular H2O2

For the past several decades, most of the research studies on nanozymes have been aimed at improving their catalytic activity and diversity; however, developing nanozymes with strong catalytic activity and great specificity remains a challenge. Herein, a simple and efficient template synthesis method was used to synthesize bimetallic sulfide nanoparticles, NiCo₂S₄ NPs, and prove that they have excellent peroxidase-like activity with good specificity. By regulating polyvinyl pyrrolidone (PVP) and hexadecyl trimethyl ammonium bromide as the templating agent, we have obtained the NiCo₂S₄ (PVP) NPs with a high Ni/Co ratio, thus exhibiting superior peroxidase activity. In addition, the NiCo₂S₄ NPs selectively catalyzed and oxidized colorless 3,3,5,5-tetramethylbenzidine (TMB). On being treated with H₂O₂, TMB turns blue while other substrates did not undergo the oxidation reaction under the same conditions, such as 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium (ABTS) and dopamine. The high specificity of NiCo₂S₄ NPs is due to the strong electrostatic driving coordination between negatively charged NiCo₂S₄ NPs and positively charged TMB. Due to the peroxidase activity of the developed NiCo₂S₄ NPs, a simple, low-cost, and reliable colorimetric method was established. Simultaneously, this method for in situ quantitative monitoring of H₂O₂ produced by MDA-MB-231 cells was also achieved. This study has provided a theoretical basis for the improvement of the activity and specificity of bimetallic sulfide nanozymes and may offer guidance for the further reasonable design of related materials.