Discovery of and Insights into DNA "Codes" for Tunable Morphologies of Metal Nanoparticles

Investigation for Regulation of a DNA-Programmed Bimetallic Nanozyme and Its Biosensing Applications

The DNA-mediated growth strategy of bimetallic nanozymes is considered as an effective approach to regulate their peroxidase activity via tuning the morphology and nanostructure. Albeit important, its biosensing application in rational methods' design and performance improvement is limited due to the deficiency of a systematic understanding of the interactions between DNA and nanomaterials used. Herein, four homo-oligonucleotides as capping ligands were employed to functionalize the bimetallic nanozymes, where Pt nanoparticles (PtNPs) were in situ synthesized onto DNA-bound Au nanorods (AuNRs), and the effects of DNA with different lengths on the state of bimetallic nanozymes were investigated in detail. It was found that the aggregation of AuNRs obviously depended on the variety and number of DNA oligonucleotides with the absorbance ratio at 810 and 525 nm (A810/A525), ranking as follows: AuNRs/A10/PtNPs > AuNRs/G10/PtNPs > AuNRs/C10/PtNPs ≫ AuNRs/T10/PtNPs, which is consistent with the value of Km for TMB, indicating that the dispersal/aggregation of the AuNRs is closely related to the deposition and growth of PtNPs, thereby significantly influencing their peroxidase activity. According to our discoveries, a novel colorimetric array platform was fabricated using the above four types of DNA-encoded Pt-Au bimetallic nanozymes as sensing elements for sensitively discriminating the five biological thiols (l-cys, GSH, Hcy, DTT, and Cys-Gly) and identifying the normal cells/tumor cells, respectively. Our work provides a new insight into DNA-programmed bimetallic nanozyme regulation and broadens its sensing applications.

Nanozymes and their biomolecular conjugates as next-generation antibacterial agents: A comprehensive review

Antimicrobial resistance (AMR), the ability of bacterial species to develop resistance against exposed antibiotics, has gained immense global attention in the past few years. Bacterial infections are serious health concerns affecting millions of people annually worldwide. Therefore, developing novel antibacterial agents that are highly effective and avoid resistance development is imperative. Among various strategies, recent developments in nanozyme technology have shown promising results as antibacterials in several antibiotic-sensitive and resistant bacterial species. Nanozymes offer several advantages over corresponding natural enzymes, such as inexpensive, stable, multifunctional, tunable catalytic properties, etc. Although the use of nanozymes as antibacterial agents has provided promising results, the specific biomolecule-conjugated nanozymes have shown further improvement in catalytic performance and associated antibacterial efficacy. The exclusive design of functional nanozymes with theranostic potential is found to simultaneously inhibit the growth and image of AMR bacterial species. This review comprehensively summarizes the history of nanozymes, their classification, biomolecules conjugated nanozyme, and their mechanism of enzyme-mimetic activity and associated antibacterial activity in antibiotic-sensitive and resistant species. The futureneeds to effectively engineer the existing or new nanozymes to curb AMR have also been discussed.

A WOx/MoOx hybrid oxide based SERS FET and investigation on its tunable SERS performance

Active control of the surface-enhanced Raman scattering (SERS) enhancement shows great potential for realizing smart detection of different molecules. However, conventional methods usually involve time-consuming structural design or a sophisticated fabrication process. Herein, we reported an electrically tunable field effect transistor (FET) comprising a WOx/MoOx hybrid as the SERS active layer. In the experiment, WOx/MoOx hybrids were first prepared by mixing different molar ratios of WOx and MoOx oxides. Then, R6G molecules were used as Raman reporters, showing that the intensity of the SERS signal observed on the most optimal hybrids (molar ratio = 1 : 3) could be increased by two times as high as that observed on a single WOx or MoOx based substrate, which was ascribed to enhanced charge transfer efficiency by the constructed nano-heterojunction between the WOx and MoOx oxides. Thereafter, a back-gate FET was fabricated on a SiO2/Si substrate, and the most optimal WOx/MoOx hybrid was deposited as the gate channel and the SERS active layer. After that, a series of gate biases (from -15 V to 15 V) were implemented to actively tune the SERS performance of the FET. It is evident that the SERS EF can be further tuned from 2.39 × 107 (-15 V) to 6.55 × 107 (+10 V), which is ∼7.4/4.1 times higher than that observed on the pure WOx device (8.81 × 106) or pure MoOx (1.61 × 107) device, respectively. Finally, the mechanism behind the electrical tuning strategy was investigated. It is revealed that a positive voltage would bend the conduction band down, which increased the electron density near the Fermi level. Consequently, it triggered the resonance charge transfer and significantly improved the SERS performance. In contrast, a negative gate voltage attracted the holes to the Fermi level, which deferred the charge transfer process, and caused the reduction of the SERS enhancement.

DNA-Encoded Bidirectional Regulation of the Peroxidase Activity of Pt Nanozymes for Bioanalysis

Rational regulation of nanozyme activity can promote biochemical sensing by expanding sensing strategies and improving sensing performance, but the design of effective regulatory strategies remains a challenge. Herein, a rapid DNA-encoded strategy was developed for the efficient regulation of Pt nanozyme activity. Interestingly, we found that the catalytic activity of Pt nanozymes was sequence-dependent, and its peroxidase activity was significantly enhanced only in the presence of T-rich sequences. Thus, different DNA sequences realized bidirectional regulation of Pt nanozyme peroxidase activity. Furthermore, the DNA-encoded strategy can effectively enhance the stability of Pt nanozymes at high temperatures, freezing, and long-term storage. Meanwhile, a series of studies demonstrated that the presence of DNA influenced the reduction degree of H₂PtCl₆ precursors, which in turn affected the peroxidase activity of Pt nanozymes. As a proof of application, the sensor array based on the Pt nanozyme system showed superior performance in the accurate discrimination of antioxidants. This study obtained the regulation rules of DNA on Pt nanozymes, which provided theoretical guidance for the development of new sensing platforms and new ideas for the regulation of other nanozyme activities.

Biological Preparation of Chitosan-Loaded Silver Nanoparticles: Study of Methylene Blue Adsorption as Well as Antibacterial Properties under Light

Human beings have made significant progress in the medical field since antibiotics were widely used. However, the consequences caused by antibiotics abuse have gradually shown their negative effects. Antibacterial photodynamic therapy (aPDT) has the ability to resist drug-resistant bacteria without antibiotics, and as it is increasingly recognized that nanoparticles can effectively solve the deficiency problem of singlet oxygen produced by photosensitizers, the application performance and scope of aPDT are gradually being expanded. In this study, we used a biological template method to reduce Ag⁺ to silver atoms in situ with bovine serum albumin (BSA) rich in various functional groups in a 50 °C water bath. The aggregation of nanomaterials was inhibited by the protein's multistage structure so that the formed nanomaterials have good dispersion and stability. It is unexpected that we used chitosan microspheres (CMs) loaded with silver nanoparticles (AgNPs) to adsorb methylene blue (MB), which is both a pollutant and photosensitive substance. The Langmuir adsorption isothermal curve was used to fit the adsorption capacity. The exceptional multi-bond angle chelating forceps of chitosan make it have a powerful physical adsorption capacity, and dehydrogenated functional groups of proteins with negative charge can also bond to positively charged MB to form a certain amount of ionic bonds. Compared with single bacteriostatic materials, the bacteriostatic capacity of the composite materials adsorbing MB under light was significantly improved. This composite material not only has a strong inhibitory effect on Gram-negative bacteria but also has a good inhibitory effect on the growth of Gram-positive bacteria poorly affected by conventional bacteriostatic agents. In conclusion, the CMs loaded with MB and AgNPs have some possible applications in the purification or treatment of wastewater in the future.

High-entropy alloy nanopatterns by prescribed metallization of DNA origami templates

High-entropy multimetallic nanopatterns with controlled morphology, composition and uniformity hold great potential for developing nanoelectronics, nanophotonics and catalysis. Nevertheless, the lack of general methods for patterning multiple metals poses a limit. Here, we develop a DNA origami-based metallization reaction system to prescribe multimetallic nanopatterns with peroxidase-like activities. We find that strong coordination between metal elements and DNA bases enables the accumulation of metal ions on protruding clustered DNA (pcDNA) that are prescribed on DNA origami. As a result of the condensation of pcDNA, these sites can serve as nucleation site for metal plating. We have synthesized multimetallic nanopatterns composed of up to five metal elements (Co, Pd, Pt, Ag and Ni), and obtained insights on elemental uniformity control at the nanoscale. This method provides an alternative pathway to construct a library of multimetallic nanopatterns.

DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications

Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.

MatOpt: A Python Package for Nanomaterials Design Using Discrete Optimization

Novel materials are being enabled by advances in synthesis techniques that achieve ever better control over the atomic-scale structure of materials. The pace of materials development has been further increased by high-throughput computational experiments guided by informatics and machine learning. We have previously demonstrated complementary approaches using mathematical optimization models to search through highly combinatorial design spaces of atomic arrangements, guiding the design of nanostructured materials. In this paper, we highlight the common features of materials optimization problems that can be efficiently modeled via mixed-integer linear optimization models. To take advantage of these commonalities, we have created MatOpt, a Python package that formalizes the process of representing the design space and formulating optimization models for the on-demand design of nanostructured materials. This tool serves to bridge the gap between practitioners with expertise in materials science and those with expertise in formulating and solving mathematical optimization models, effectively lowering the barriers for applying rigorous numerical optimization capabilities during nanostructured materials development.

One-Step, DNA-Programmed, and Flash Synthesis of Anisotropic Noble Metal Nanostructures on MXene

Precise morphological control over anisotropic noble metal nanoparticles (ANPs) is one of the key issues in the nano-research field owing to their unique optoelectronic, magnetic, mechanical, and catalytic properties. Although nanostructures fabricated by the directed assembly of adsorbate have been widely demonstrated recently, facile yet universal synthesis of nanocrystal with tunable morphologies, green templates, no seeds, and high yield remains challenging. Herein, we develop a versatile method, allowing for the rapid, one-step, seedless, surfactant-free synthesis of a noble metal nanostructure with tunable anisotropy on MXene in a sequence-dependent manner through a single-DNA molecular regulator. Based on the mild reducibility of MXene and the selective affinity of the DNA to the specific facets in the crystals, oriented aggregations and the growth of ANPs (Au, Pt, Pd) can be achieved and the resulting asymmetric morphology from polyhedrons, or flowers, or nanoplates to dendrites is observed. The ability to align such ANPs on the MXene surface is expected to lead to improved photothermal effect and surface-enhanced Raman scattering. Furthermore, our work makes the fabrication of the ANPs or ANP-MXene heterostructure easier, stimulating further explorations of physical, chemical, and biological applications.

DNA-encoded bimetallic Au-Pt dumbbell nanozyme for high-performance detection and eradication of Escherichia coli O157:H7

Infectious Escherichia coli O157:H7 threatens the health of millions people each year. Thus, it is important to establish a simple and sensitive method for bacterial detection and eradication. Herein, a DNA-programming strategy is explored to synthesize anisotropic dumbbell-like Au-Pt nanoparticles with excellent catalytic and anti-bacterial activities, which were applied in the simultaneous detection and eradication of pathogenic bacteria. The DNA sequence-dependent growth of bimetallic nanoparticles is firstly studied and polyT20 has the tendency to form dumbbell-like Au-Pt bimetallic structures based on gold nanorods seeds. PolyA20 and polyC20 can also form similar structures but only at much lower DNA concentrations, which can be explained by their much higher affinity to the metal surfaces than T20. The as-prepared nanoparticles exhibit high nanozyme catalytic activity resulting from the synergistic effect of Au and Pt. Under light irradiation, the Au-Pt nanoparticles show high photothermal conversion efficiency and enhanced catalytic activity, which can be applied for the eradication and detection of E. coli O157:H7 with a robust efficacy (95%) in 5 min and provides excellent linear detection (10-10⁷ CFU/mL), with a detection limit of 2 CFU/mL. This study offered new insights into DNA-directed synthesis of nanomaterials with excellent biosensing and antibiotic applications.

Controllable Synthesis of Bimetallic Nanostructures Using Biogenic Reagents: A Green Perspective

Bimetallic nanostructures are emerging as a significant class of metal nanomaterials due to their exceptional properties that are useful in various areas of science and technology. When used for catalysis and sensing applications, bimetallic nanostructures have been noted to exhibit better performance relative to their monometallic counterparts owing to synergistic effects. Furthermore, their dual metal composition and configuration can be modulated to achieve optimal activity for the desired functions. However, as with other nanostructured metals, bimetallic nanostructures are usually prepared through wet chemical routes that involve the use of harsh reducing agents and hazardous stabilizing agents. In response to intensifying concerns over the toxicity of chemicals used in nanomaterial synthesis, the scientific community has increasingly turned its attention toward environmentally and biologically compatible reagents that can enable green and sustainable nanofabrication processes. This article aims to provide an evaluation of the green synthetic methods of constructing bimetallic nanostructures, with emphasis on the use of biogenic resources (e.g., plant extracts, DNA, proteins) as safe and practical reagents. Special attention is devoted to biogenic synthetic protocols that demonstrate controllable nanoscale features, such as size, composition, morphology, and configuration. The potential use of these biogenically prepared bimetallic nanostructures as catalysts and sensors is also discussed. It is hoped that this article will serve as a valuable reference on bimetallic nanostructures and will help fuel new ideas for the development of more eco-friendly strategies for the controllable synthesis of various types of nanostructured bimetallic systems.

Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications

Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.

Regulating Catalytic Activity of DNA-Templated Silver Nanoclusters Based on their Differential Interactions with DNA Structures and Stimuli-Responsive Structural Transition

This work reports exquisite engineering of catalytic activity of DNA-templated silver nanoclusters (DNA-AgNCs) based on unique adsorption phenomena of DNAs on DNA-AgNCs and reversible transition between double and triple-stranded DNAs. Four DNA homopolymers exhibit different inhibition effects on the catalytic activity of DNA-AgNCs, poly adenine (polyA) > poly guanine (polyG) > poly cytosine (polyC) > poly thymine (polyT), demonstrating that polyA strands have the strongest adsorption affinity on DNA-AgNCs. Through the formation of T-A•T triplex DNAs, catalytic activity of DNA-AgNCs is restored from the deactivated state by double or single-stranded DNAs, indicating the participation of N7 groups of adenine bases in binding to DNA-AgNCs and blocking active sites. Accordingly, reversibly regulating catalytic activity of DNA-AgNCs can be realized based on DNA input-stimulated transition between duplex and triplex structures. In the end, two low-cost and facile biosensing methods are presented, which are derived from the activity-switchable platform. It is worthy to anticipate that the DNA-AgNCs with controlled catalytic activity will inspire researchers to devise more functionalized nanocatalysts and contribute to the exploration of intelligent biomedicine in the future.

Prominence of the Instability of a Stabilizing Agent in the Changes in Physical State of a Hybrid Nanomaterial

Shaping ability of hybrid nanomaterials is a key point for their further use in devices. It is therefore crucial to control it. To this end, it is necessary that the macroscopic properties of the material remain constant over time. Here, we evidence by multinuclear Magic-Angle Spinning Nuclear Magnetic Resonance spectroscopic study including ¹⁷ O isotope exchange that for a ZnO-alkylamine hybrid material, the partial carbonation of amine into ammonium carbamate molecules is behind the conversion from highly viscous liquid to a powdery solid when exposed to air. This carbonation induces modification and reorganization of the organic shell around the nanocrystals and affects significantly the macroscopic properties of the material such as it physical state, its solubility and colloidal stability. This study, straightforwardly extendable, highlights that the nature of the functional chemical group allowing connecting the stabilizing agent (SA) to the surface of the nanoparticles is of tremendous importance especially if the SA is reactive with molecules present in the environment.

Capping Ligand Size-Dependent LSPR Property Based on DNA Nanostructure-Mediated Morphological Evolution of Gold Nanorods for Ultrasensitive Visualization of Target DNA

Systematically tuning the structures and properties of noble-metal nanoparticles through biomolecule-mediated overgrowth is of significant importance for their applications in biosensing and imaging. Herein thiolated biomolecules with different concentrations and sizes (molecular weight and spatial structure) were used as a class of capping ligands to control the longitudinal surface plasmon resonance (LSPR) property of gold nanorods (GNRs). The LSPR peaks were red-shifted by increasing the capping agent concentration. The size effect could be divided to two aspects: (1) When the ligands are small molecules, the LSPR peak is blue-shifted as the size of the capping ligand increases. (2) When the ligands are macromolecular proteins, the LSPR property is similar to that of the overgrown nanoparticle (Au@gap@GNR) without thiolated biomolecules as capping agents. Interestingly, thiol-free and nonhomooligomeric DNA strands as capping agents present a similar influence in shaping the overgrowth of GNRs by varying their concentrations and sizes. In addition, the size effect of a DNA nanostructure was used to construct a Δλ_LSPR-based catalytic nucleic acid biosensor using a DNA dendritic nanostructure as a capping agent combined with LSPR signals generated from the Au@gap@GNRs with morphological evolution. More importantly, the Δλ_LSPR-based biosensor possesses three advantages in nucleic acid biosensing: (1) It is completely label- and wash-free, (2) it has an ultrahigh sensitivity and signal-to-noise ratio, and (3) it can be visualized without any instrumental aid, indicating a significant potential for ultrasensitive biosensing.

Gold Nanobones Enhanced Ultrasensitive Surface-Enhanced Raman Scattering Aptasensor for Detecting Escherichia coli O157:H7

Sensitive, robust, and highly specific detection of Escherichia coli O157:H7, one of the most hazardous foodborne pathogens and the cause of numerous diseases, is needed to ensure public health. Herein, a one-pot step method is reported for the preparation of multifunctional gold nanobones (NBs) (GNR_Apt-1+RhB) from gold nanorods (GNRs) comediated by an aptamer (Apt-1) and the signal molecule rhodamine B (RhB) for surface-enhanced Raman scattering detection of E. coli O157:H7. The characterized result showed that Apt-1 and RhB were embedded in the gold NBs, and then, this combination exhibited good recognition, excellent stability, and significant Raman signal intensity enhancement. The Raman enhancement derived from a strong electromagnetic field distribution with the locations at the apex of both ends of the GNR_Apt-1+RhB and the signal stability was because of the firm embedment of Apt-1 (poly A20 + E. coli O157:H7 aptamers) and RhB on the surface of the GNR_Apt-1+RhB. Optimization experiments established that surface-enhanced Raman-scattered RhB absorption at 1350 cm^-1 had a strong linear relationship (y = 180.30x - 61.49; R² = 0.9982) with E. coli O157:H7 concentration over the range of 10-10,000 cfu/mL with a limit of detection of 3 cfu/mL. This novel aptasensor sensitively detects E. coli O157:H7 and has great promise for food pathogenic bacteria detection.

Bioapplications of DNA nanotechnology at the solid-liquid interface

DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.