Synthesis of Branched DNA Scaffolded Super-Nanoclusters with Enhanced Antibacterial Performance

Antibiotic Alternatives: Multifunctional Ultra-Small Metal Nanoclusters for Bacterial Infectious Therapy Application

The prevalence of major bacterial infections has emerged as a significant menace to human health and life. Conventional treatment methods primarily rely on antibiotic therapy, but the overuse of these drugs has led to a decline in their efficacy. Moreover, bacteria have developed resistance towards antibiotics, giving rise to the emergence of superbugs. Consequently, there is an urgent need for novel antibacterial agents or alternative strategies to combat bacterial infections. Nanoantibiotics encompass a class of nano-antibacterial materials that possess inherent antimicrobial activity or can serve as carriers to enhance drug delivery efficiency and safety. In recent years, metal nanoclusters (M NCs) have gained prominence in the field of nanoantibiotics due to their ultra-small size (less than 3 nm) and distinctive electronic and optical properties, as well as their biosafety features. In this review, we discuss the recent progress of M NCs as a new generation of antibacterial agents. First, the main synthesis methods and characteristics of M NCs are presented. Then, we focus on reviewing various strategies for detecting and treating pathogenic bacterial infections using M NCs, summarizing the antibacterial effects of these nanoantibiotics on wound infections, biofilms, and oral infections. Finally, we propose a perspective on the remaining challenges and future developments of M NCs for bacterial infectious therapy.

Smart Enzyme-Like Polyphenol-Copper Spray for Enhanced Bacteria-Infected Diabetic Wound Healing

Developing functional medical materials is urgent to treat diabetic wounds with a high risk of bacterial infections, high glucose levels and oxidative stress. Here, a smart copper-based nanocomposite acidic spray has been specifically designed to address this challenge. This copper-based nanocomposite is pH-responsive and has multienzyme-like properties. It enables the spray to effectively eliminate bacteria and alleviate tissue oxidative pressure, thereby accelerating the healing of infected diabetic wounds. The spray works by generating hydroxyl radicals through catalysing H2O2, which has a high sterilization efficiency of 97.1%. As alkaline micro-vessel leakage neutralizes the acidic spray, this copper-based nanocomposite modifies its enzyme-like activity to eliminate radicals. This reduces the level of reactive oxygen species in diabetic wounds by 45.3%, leading to a similar wound-healing effect between M1 diabetic mice and non-diabetic ones by day 8. This smart nanocomposite spray provides a responsive and regulated microenvironment for treating infected diabetic wounds. It also offers a convenient and novel approach to address the challenges associated with diabetic wound healing.

Tobramycin-mediated self-assembly of DNA nanostructures for targeted treatment of Pseudomonas aeruginosa-infected lung inflammation

Pseudomonas aeruginosa (PA) is one of the most common multidrug-resistant pathogens found in clinics, often manifesting as biofilms. However, due to the emergence of superbugs in hospitals and the overuse of antibiotics, the prevention and treatment of PA infections have become increasingly challenging. Utilizing DNA nanostructures for packaging and delivering antibiotics presents an intervention strategy with significant potential. Nevertheless, construction of functional DNA nanostructures with multiple functionalities and enhanced stability in physiological settings remains challenging. In this study, the authors propose a magnesium-free assembly method that utilizes tobramycin (Tob) as a mediator to assemble DNA nanostructures, allowing for the functionalization of DNA nanostructures by combining DNA and antibiotics. Additionally, our study incorporates maleimide-modified DNA into the nanostructures to act as a targeting moiety specifically directed towards the pili of PA. The targeting ability of the constructed functional DNA nanostructure significantly improves the local concentration of Tob, thereby reducing the side effects of antibiotics. Our results demonstrate the successful construction of a maleimide-decorated Tob/DNA nanotube (NTTob-Mal) for the treatment of PA-infected lung inflammation. The stability and biocompatibility of NTTob-Mal are confirmed, highlighting its potential for clinical applications. Furthermore, its specificity in recognizing and adhering to PA has been validated. In vitro experiments have shown its efficacy in inhibiting PA biofilm formation, and in a murine model, NTTob-Mal has exhibited significant therapeutic effectiveness against PA-induced pneumonia. In summary, the proposed antibiotic drug-mediated DNA nanostructure assembly approach holds promise as a novel strategy for targeted treatment of PA infections.

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

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

Potential mechanism of the AgNCs-hydrogel in promoting the regeneration of diabetic infectious wounds

Diabetic infectious wound treatment is challenging due to insistent wound infections. To treat such complicated pathological diabetic infectious wounds, multifunctional materials need to be developed, and their mechanisms need to be understood. Here, we developed a material termed AgNCs-hydrogel, which is a multifunctional DNA hydrogel used as dressings by integrating it with antibacterial silver nanoclusters. The AgNCs-hydrogel was applied to promote the regeneration of diabetic infectious wounds in mice because it exhibited superior antibacterial activity and effective ROS-scavenging properties. Based on skin proteomics, we explored the potential mechanism of the AgNCs-hydrogel in treating mouse skin wounds. We found that the AgNCs-hydrogel can regulate some key proteins located primarily in the extracellular exosomes, involved in the negative regulation of the apoptotic process, and perform ATP binding to accelerate diabetic infected wound closure. Therefore, this study provided a multifunctional AgNCs-hydrogel and revealed its potential mechanism in promoting the regeneration of diabetic infectious wounds.

DNA-Based Hydrogels with Multidrug Sequential Release for Promoting Diabetic Wound Regeneration

Diabetic wound (DW) regeneration is highly challenging due to persistent bacterial infection, excessive production of reactive oxygen species (ROS), prolonged inflammatory response, and insufficient angiogenesis. Ideal management requires the integration and sequential release of bactericidal, antioxidative, anti-inflammatory, and angiogenic agents during DW repair. Here, we develop a DNA-based multidrug hydrogel, termed Agilegel, to promote the efficient healing of DW. Hierarchically structured Agilegel can precisely control the sequential release of vascular endothelial growth factor-alpha (VEGF-α), silver nanoclusters (AgNCs), and interleukin-10 (IL-10) through covalent bonds in its primary structure (phosphate backbone), noncovalent bonds in its secondary structure (base pairs), and physical encapsulation in its advanced structure (pores), respectively. We demonstrate that Agilegel can effectively eliminate bacterial infection through AgNCs and mitigate ROS production through DNA scaffolds. Moreover, during the inflammatory phase, Agilegel promotes the polarization of macrophages from pro-inflammatory M1 to anti-inflammatory M2 phenotype using IL-10. Subsequently, Agilegel stimulates cell proliferation, angiogenesis, and extracellular matrix formation through the action of VEGF-α, thereby accelerating the closure of DW. Our results indicate that DNA hydrogels confer the capacity to regulate the sequential release of drugs, enabling them to effectively manage the phased intervention of multiple drugs in the treatment of complex diseases within physiological environments.

Optical, structural and antibacterial properties of silver nanoparticles and DNA-templated silver nanoclusters

Silver nanoparticles (AgNPs) are increasingly considered for biomedical applications as drug-delivery carriers, imaging probes and antibacterial agents. Silver nanoclusters (AgNCs) represent another subclass of nanoscale silver. AgNCs are a promising tool for nanomedicine due to their small size, structural homogeneity, antibacterial activity and fluorescence, which arises from their molecule-like electron configurations. The template-assisted synthesis of AgNCs relies on organic molecules that act as polydentate ligands. In particular, single-stranded nucleic acids reproducibly scaffold AgNCs to provide fluorescent, biocompatible materials that are incorporable in other formulations. This mini review outlines the design and characterization of AgNPs and DNA-templated AgNCs, discusses factors that affect their physicochemical and biological properties, and highlights applications of these materials as antibacterial agents and biosensors.

Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures

Molecular dynamics (MD) simulations can be used to investigate the stability and conformational characteristics of RNA nanostructures. However, MD simulations of an RNA nanostructure is computationally expensive due to the size of nanostructure and the number of atoms. Alternatively, MD simulations of RNA motifs can be used to estimate the conformational stability of constructed RNA nanostructure due to their small sizes. In this chapter, we introduce the preparation and MD simulations of two RNA kissing loop (KL) motifs, a linear KL complex and a bent KL complex, and an RNA nanoring. The initial solvated system and topology files of each system will be prepared by two major force fields, AMBER and CHARMM force fields. MD simulations will be performed by NAMD simulation package, which can accept both force fields. In addition, we will introduce the use of the AMBER cpptraj program and visual molecular dynamics (VMD) for data analysis. We will also discuss how MD simulations of two KL motifs can be used to estimate the conformation and stability of RNA nanoring as well as to explain the vibrational characteristics of RNA nanoring.

Inhibition of Bacteria In Vitro and In Vivo by Self-Assembled DNA-Silver Nanocluster Structures

Antimicrobial nanomaterials hold great promise for bacteria-infected wound healing. However, it remains a challenge to balance antimicrobial efficacy and biocompatibility for these artificial antimicrobials. Here we employed biocompatible genetic molecule DNA as a building material to fabricate antimicrobial materials, including self-assembled Y-shaped DNA-silver nanocluster composite (Y-Ag) and Y-Ag hydrogel (Y-Ag-gel). We demonstrate that macroscopic and microcosmic DNA-Ag composites can effectively inhibit bacterial growth but do not affect cell proliferation in vitro. In particular, Y-Ag spray can speed up the process of wound healing in vivo. Considering the efficacy and advantages of DNA-based materials, our findings provide a promising route to fabricate a novel wound dressing such as spray and hydrogel for therapeutic wound healing.

Antibacterial metal nanoclusters

Combating bacterial infections is one of the most important applications of nanomedicine. In the past two decades, significant efforts have been committed to tune physicochemical properties of nanomaterials for the development of various novel nanoantibiotics. Among which, metal nanoclusters (NCs) with well-defined ultrasmall size and adjustable surface chemistry are emerging as the next-generation high performance nanoantibiotics. Metal NCs can penetrate bacterial cell envelope more easily than conventional nanomaterials due to their ultrasmall size. Meanwhile, the abundant active sites of the metal NCs help to catalyze the bacterial intracellular biochemical processes, resulting in enhanced antibacterial properties. In this review, we discuss the recent developments in metal NCs as a new generation of antimicrobial agents. Based on a brief introduction to the characteristics of metal NCs, we highlight the general working mechanisms by which metal NCs combating the bacterial infections. We also emphasize central roles of core size, element composition, oxidation state, and surface chemistry of metal NCs in their antimicrobial efficacy. Finally, we present a perspective on the remaining challenges and future developments of metal NCs for antibacterial therapeutics.

Conjugating AIE-featured AuAg nanoclusters with highly luminescent carbon dots for improved visible-light-driven antibacterial activity

Metal nanoclusters (NCs) have emerged as novel antibacterial agents featuring broad-spectrum antibacterial activity without drug resistance for bacteria, but suffer from fast antibacterial invalidation due to their consumption by bacteria. Herein we report the design of a visible-light-driven photodynamic antibacterial agent based on conjugating aggregation-induced emission (AIE)-featured AuAg NCs with highly luminescent carbon dots (CDs). The conjugation of CDs with AuAg NCs could not only enhance the visible-light harvest, but also promote charge carrier generation/separation via charge/energy transfer, leading to the production of abundant reactive oxygen species (ROS) for bacterial killing under visible-light irradiation. Consequently, the as-obtained CDs@AuAg NCs display excellent photodynamic antibacterial activity against both Gram-positive and Gram-negative bacteria with 4-5 orders of magnitude reduction in colony forming units, which is different from the conventional metal NC-based analogue relying on self-consumption for bacterial killing. In addition, the CDs@AuAg NCs are found to be free of cytotoxicity; the ROS capture experiments indicate that the photoproduced H₂O₂ by CDs@AuAg NCs is the main active species for bacterial killing, accounting for nearly 48% of the total antibacterial efficacy. This study provides a paradigm for the design of metal NC-based photodynamic antibacterial agents for diverse bactericidal applications.

Modulating the Fluorescence of Silver Nanoclusters Wrapped in DNA Hairpin Loops via Confined Strand Displacement and Transient Concatenate Ligation for Amplifiable Biosensing

It is intriguing to modulate the fluorescence emission of DNA-scaffolded silver nanoclusters (AgNCs) via confined strand displacement and transient concatenate ligation for amplifiable biosensing of a DNA segment related to SARS-CoV-2 (s₂DNA). Herein, three stem-loop structural hairpins for signaling, recognizing, and assisting are designed to assemble a variant three-way DNA device (3WDD) with the aid of two linkers, in which orange-emitting AgNC (oAgNC) is stably clustered and populated in the closed loop of a hairpin reporter. The presence of s₂DNA initiates the toehold-mediated strand displacement that is confined in this 3WDD for repeatable recycling amplification, outputting numerous hybrid DNA-duplex conformers that are implemented for a transient "head-tail-head" tandem ligation one by one. As a result, the oAgNC-hosted hairpin loops are quickly opened in loose coil motifs, bringing a significant fluorescence decay of multiple clusters dependent on s₂DNA. Demonstrations and understanding of the tunable spectral performance of a hairpin loop-wrapped AgNC via switching 3WDD conformation would be highly beneficial to open a new avenue for applicable biosensing, bioanalysis, or clinical diagnostics.

Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering

Branched DNA with multibranch-like anisotropic topology serves as a promising and powerful building block in constructing multifunctional-integrated nanomaterials in a programmable and controllable manner. Recently, a series of branched DNA-based functional nanomaterials were developed by elaborate molecular design. In this review, we focused on the construction of branched DNA-based nanostructures for biological and biomedical applications. First, the molecular design and synthesis method of branched DNA monomer were briefly described. Then, the construction strategies of branched DNA-based nanostructures were categorially discussed, including target-triggered polymerization, enzymatic extension and hybrid assembly. Finally, the biological and biomedical applications including diagnosis, therapeutics and protein engineering were summarized. We envision that the review will contribute to the further development of branched DNA-based nanomaterials with great application potential in the field of biomedicine, thus building a new bridge between material chemistry and biomedicine.

Multibranched Linear DNA-Controlled Assembly of Silver Nanoclusters and Their Applications in Aptamer-Based Cell Recognition

DNA-templated silver nanoclusters (DNA-AgNCs) are promising fluorescent materials and have been used in cancer diagnosis. Although many different DNA-AgNC applications have been realized, most of them rely on individual DNA-AgNCs or assembled DNA-AgNCs with limited recognition abilities, resulting in low detection sensitivity or off-target effects, in turn, hindering the performance of DNA-AgNCs in cancer cell recognition. As a solution, we assembled DNA-AgNCs by a multibranched linear (MBL) DNA structure formed through a trigger-initiated hybridization chain reaction (HCR) regarding the natural compatibility of DNA-AgNCs with DNA programmability and the advantages of DNA assembly in incorporating repetitive and functional moieties into one structure. By the specific modification of the trigger, MBL-AgNCs tethered with the targeting aptamer and partially hybridized duplex, which works as a component of DNA logic platform relying on the combination of cascade strand displacement reaction and specific recognition ability of aptamers, were obtained, respectively. DNA-AgNCs assembled by the aptamer-tethered MBL structure exhibited about 20-fold enhanced detection sensitivity in recognizing cancer cells compared to individual aptamer-tethered DNA-AgNCs. DNA-AgNCs assembled by the duplex-attached MBL exhibited logic performance in analyzing dual cell surface receptors with the assistance of "AND" logic platform, thus identifying cancer cells with high sensitivity and resolution. The facile conjugation of the MBL structure with different functional DNA structures makes it an ideal platform to assemble DNA-AgNCs used for aptamer-based cell recognition, thus broadening the potential applications of DNA-AgNCs.

Amplifiable ratiometric fluorescence biosensing of nanosilver multiclusters populated in three-way-junction DNA branches

To explore the fluorescence bio-responsiveness of emissive silver nanoclusters (AgNCs) populated in DNA-branched scaffolds is intriguing yet challenging. In response to a desired targeting model (T*) as a vehicle, herein a customized three-way-junction DNA construct (TWJDC) is assembled via competitive hybridizing cascade among three stem-loop hairpins with specific base sequences, where the repeated recycling of T* enables the exponentially amplifiable output of rigid TWJDC. As designed, these stable hybridization products are highly T*-stimulated responsive and constructing-directional. In the three branched-arms, the unpaired sticky ends provide isotropic binding sites for a signaling hairpin encoded with two C-rich templates of green- and red-AgNCs clustering. The identical ligation of signal probe with three arms of TWJDC liberates its locked stem, enabling the separate growth of red-clusters in three branches. As demonstrated, three clusters of red-AgNCs possess advantageous self-enhancing fluorescent performance relative to single or two cluster(s), good biocompatibility and low cytotoxicity. Utilizing the bicolor AgNCs as dual-emitters with reversely changed emission intensity, we developed an innovative ratiometric strategy displaying sensitively linear dose-dependence on variable T* down to 1.9 pM, which can afford a promising platform for biosensing, bioanalysis, cell imaging, or even clinical theranostics.

Self-extending DNA-Mediated Isothermal Amplification System and Its Biosensing Applications

Signal amplification is critical to achieving sensitive biosensing, but complex strategies often bring problems like system instability, false positive, or narrow target spectrum. Here, a self-extending DNA-mediated isothermal amplification (SEIA) system with simple reaction components is introduced to achieve rapid, robust, and significant signal amplification. In SEIA, based on spontaneous refolding of specific DNA domains and using the previous generation product as a template, a DNA strand can extend continuously in an approximate exponential growth pattern, which was accurately predicted by our formula and well supported by AFM results. Based on a set of proof-of-concept experiments, it was proved that the SEIA system can output different signals and flexibly integrate various functional nucleic acids, which makes it suitable for different scenarios and realizes broad-spectrum target detection. Taking into account the advantages of simplicity, flexibility, and efficiency, the SEIA system as an independent signal amplification module will enrich the toolbox of biosensing design.

Aptamer-Functionalized DNA-Silver Nanocluster Nanofilm for Visual Detection and Elimination of Bacteria

As a new type of nanomaterial, DNA-templated silver nanoclusters (DNA-AgNCs) have been widely studied because of their fluorescence and antibacterial properties. In this study, we combined the DNA-AgNCs with aptamers of bacteria to achieve a novel approach for the visual detection and effective elimination of bacteria. The aptamers of Staphylococcus aureus (S. aureus) were linked to G-rich sequences to achieve fluorescence enhancement when approaching the DNA-AgNCs. The capture of aptamers not only realized the visual monitoring of bacteria but also promoted the antibacterial effects. Additionally, a fluorescent nanofilm with excellent selectivity and antibacterial activity in the detection and elimination of S. aureus was developed based on the DNA-AgNCs. These aptamer-functionalized DNA-AgNCs show significant potential for many applications in food packaging and biomedical engineering.

Antibacterial mechanism and transcriptome analysis of ultra-small gold nanoclusters as an alternative of harmful antibiotics against Gram-negative bacteria

In this work, a well-known Au₂₅ NCs with high purity was prepared by simple one-pot reducing method. The as-synthesized Au₂₅ NCs exhibited excellent antibacterial efficiency toward Gram-negative bacteria in a dose- and time-dependent manner, which could be used as nanoantibiotics to replace harmful antibiotics. The antibacterial assays showed that almost 100% bacteria were killed at lower concentration (100-150 μM) within a short time (30-60 min), providing a rapid and effective killing outcome for Gram-negative bacteria. After that, antibacterial mechanism was mainly investigated at cellular level via destruction of membrane integrity, disruption of antioxidant defense system, metabolic inactivation, DNA damage, as well as at molecular level via transcriptome analysis (RNA sequencing) for the first time. RNA sequencing results showed that differentially expressed genes (DEGs) related to biosynthesis of cell wall and membrane, glycolysis and TCA cycle, oxidative phosphorylation and DNA replication and repair were significantly affected. It was concluded that synergetic effect of membrane damage, oxidative stress, DNA damage and energy metabolism eventually led to the Gram-negative bacteria growth inhibition and death.

DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells

Silver has a long history of antibacterial effectiveness. The combination of atomically precise metal nanoclusters with the field of nucleic acid nanotechnology has given rise to DNA-templated silver nanoclusters (DNA-AgNCs) which can be engineered with reproducible and unique fluorescent properties and antibacterial activity. Furthermore, cytosine-rich single-stranded DNA oligonucleotides designed to fold into hairpin structures improve the stability of AgNCs and additionally modulate their antibacterial properties and the quality of observed fluorescent signals. In this work, we characterize the sequence-specific fluorescence and composition of four representative DNA-AgNCs, compare their corresponding antibacterial effectiveness at different pH, and assess cytotoxicity to several mammalian cell lines.

Highly efficient nanomedicine from cationic antimicrobial peptide-protected Ag nanoclusters

Designing the homogeneous assembly of the bio-nano interface to fine-tune the interactions between the nanoprobes and biological systems is of prime importance to improve the antimicrobial efficiency of nanomedicines. In this work, highly luminescent silver nanoclusters with the homogeneous conjugation of an antimicrobial peptide (referred to as Dpep-Ag NCs) were achieved via the reduction-decomposition-reduction process as a single package. The as-designed Dpep-Ag NCs inherited the two distinctive features of bactericides from the Ag+ species and the antimicrobial peptide of Dpep, and exhibited enhanced bacterial killing efficiency compared with other control groups including BSA-capped Ag NCs and the original antimicrobial peptide bactenecin (Opep)-protected Ag nanoparticles (Opep-Ag NPs). The ultrasmall size feature of Dpep-Ag NCs combined with the positively charged bactericidal tail allow a better interface and interaction with the cell membrane owing to the selective targeting of lipopolysaccharides in the Gram-negative bacteria and electrostatic interaction, facilitating the membrane permeability. Dpep-Ag NCs restrained the E. coli growth visibly and outperformed commercial Ag NPs (30 nm) with reduced (ca. 100-fold) minimal inhibitory concentration. The analysis of infected wound sizes and tissues treated with Dpep-Ag NCs in a murine model reveal obvious differences in the healing effect compared with the other counterparts, demonstrating its antibacterial efficiency in practical application.

Recent advances in templated synthesis of metal nanoclusters and their applications in biosensing, bioimaging and theranostics

As a kind of promising nanomaterials, metal nanoclusters (MNCs) generally composed of several to hundreds of metal atoms have received increasing interest owing to their unique properties, such as ultrasmall size (<2 nm), fascinating physical and chemical properties, and so on. Recently, template-assisted synthesis of MNCs (e.g., Au, Ag, Cu, Pt and Cd) has attracted extensive attention in biological fields. Up to now, various templates (e.g., dendrimers, polymers, DNAs, proteins and peptides) with different configurations and spaces have been applied to prepare MNCs with the advantages of facile preparation, controllable size, good water-solubility and biocompatibility. Herein, we focus on the recent advances in the template-assisted synthesis of MNCs, including the templates used to synthesize MNCs, and their applications in biosensing, bioimaging, and disease theranostics. Finally, the challenges and future perspectives of template-assisted synthesized MNCs are highlighted. We believe that this review could not only arouse more interest in MNCs but also promote their further development and applications by presenting the recent advances in this area to researchers from various fields, such as chemistry, material science, physiology, biomedicine, and so on.

DNA pom-pom nanostructure as a multifunctional platform for pathogenic bacteria determination and inactivation

Pathogenic bacteria levels are significantly related with disease control, clinical diagnosis, and even environmental monitoring. It is becoming highly urgent to achieve ultrasensitive detection of pathogenic bacteria and efficient combat of bacterial infection. Toward this end, we have assembled a DNA Pom-Pom nanostructure (PP-N) based multifunctional platform for pathogenic bacteria determination and inactivation. In particular, one DNA oligonucleotide probe that serve as a trigger was specifically designed for the autonomous cross-opening of metastable DNA hairpin probes and long dsDNA structure formation, achieving a catalytic self-assembly of DNA nanostructure. Numerous DNA strands in this PP-N assembly provide sufficient interaction sites for functional domains and connector, showing high programmability, excellent biostability, as well as selective target recognition. With these properties, the fluorescence dyes modified PP-N platform showed excellent bacteria analysis with both excellent selectivity and ultrasensitive determination limit as low as 2.0 CFU/mL. Furthermore, the aptamer-functionalized and antibiotics loaded PP-N platform demonstrate excellent merits of high antibiotics-loading capacity and negligible cytotoxicity to targets. Therefore, this DNA PP-N assembly based multifunctional platform promise its great application in targeted sensing, combating bacterial infection, and potential clinic therapy.

The spatial organization of trace silver atoms on a DNA template

DNA with programmable information can be used to encode the spatial organization of silver atoms. Based on the primary structures of a DNA template containing a controllable base arrangement and number, the surrounding environment and cluster together can induce the folding of the DNA template into an appropriate secondary structure for forming AgNCs with different fluorescence emissions, such as i-motif, G-quadruplex, dimeric template, triplex, monomeric or dimeric C-loop, emitter pair, and G-enhancer/template conjugate. Stimuli can induce the dynamic structural transformation of the DNA template with a recognition site for favourably or unfavourably forming AgNCs, along with varied fluorescence intensities and colours. The array of several or more of the same and different clusters can be performed on simple and complex nanostructures, while maintaining their original properties. By sorting out this review, we systematically conclude the link between the performance of AgNCs and the secondary structure of the DNA template, and summarize the precise arrangement of nanoclusters on DNA nanotechnology. This clear review on the origin and controllability of AgNCs based on the secondary structure of the DNA template is beneficial for exploring the new probe and optical devices.

Development of coinage metal nanoclusters as antimicrobials to combat bacterial infections

Infections from antibiotic-resistant bacteria have caused huge economic loss and numerous deaths over the past decades. Researchers are exploring multiple strategies to combat these bacterial infections. Metal nanomaterials have been explored as therapeutics against these infections owing to their relatively low toxicity, broad-spectrum activity, and low bacterial resistance development. Some coinage metal nanoclusters, such as gold, silver, and copper nanoclusters, can be readily synthesized. These nanoclusters can feature multiple useful properties, including ultra-small size, high catalytic activity, unique photoluminescent properties, and photothermal effect. Coinage metal nanoclusters have been investigated as antimicrobials, but more research is required to tap their full potential. In this review, we discuss multiple advantages and the prospect of using gold/silver/copper nanoclusters as antimicrobials.

Label-Free Analysis of H5N1 Virus Based on Three-Segment Branched DNA-Templated Fluorescent Silver Nanoclusters

Since H5N1 virus is a highly infectious pathogen that causes outbreaks of avian influenza, developing a sensitive and rapid diagnostic platform to sense it becomes significant. Here, a novel label-free fluorescence sensing platform based on DNA-templated silver nanoclusters (DNA-Ag NCs) is developed to detect the H5N1 gene sequence representing H5N1 virus. The three-segment-branched DNA structure with closed cytosine-rich loop is designed as an effective template to produce fluorescent Ag NCs, which is different with the previous design of cytosine-rich loop formed by hairpin-like single-stranded DNA or double-stranded DNA. The proposed fluorescence detection approach gives a wide linear range (500 pM-2 μM) and a low detection limit (500 pM) to sense H5N1 gene sequence. Furthermore, selective analysis of target DNA shows that our constructed analytical strategy has a high selectivity to H5N1 gene sequence. It is regarded as a promising method for highly sensitive and selective sensing of H5N1 virus.

Selective recognition of CdTe QDs and strand displacement signal amplification-assisted label-free and homogeneous fluorescence assay of nucleic acid and protein

Due to their simplicity of design and operation, homogeneous bioassays have been of great interest to researchers. Herein, a label-free and free separation fluorescence sensing platform was constructed for the determination of nucleic acid and prostate specific antigen (PSA) using CdTe QDs as the signal molecule. In our previous work, we surprisingly found that the CdTe QDs can selectively distinguish Ag+ and the C-Ag+-C complex, which was the basis of the sensor. On the basis of the selective cation exchange reaction (CER), combined with the signal amplification of the strand displacement reaction (SDR), this work was first applied for the sensitive analysis of DNA. There are two types of hairpin structures in this sensing system, including the recognition probe (HP) and Ag+, which formed the C-Ag+-C structure, and the hairpin structure formed by the helper DNA itself. In this work, target DNA can trigger the SDR that generates lots of HP-helper double-stranded DNA (dsDNA) and recycles the target DNA while releasing a large amount of Ag+, thus quenching the fluorescence signal of CdTe QDs to achieve the highly sensitive detection of DNA. In order to verify the versatility of this system using DNA as a bridge and aptamers as recognition probes, we extended the system to the detection of PSA. After examining its experimental performance, it was determined that this method displayed good analytical capability for DNA in the range of 10-13-10-10 M and PSA in the range of 10-13-10-10 g mL-1 with low 25 fM and 30 fg mL-1 limits of detection (LODs), respectively; high selectivity for both the target sequence and protein was shown. In addition, this platform was successfully used for the analysis of PSA in serum samples.

DNA-Hairpin-Templated Silver Nanoclusters: A Study on Stem Sequence

DNA hairpins are widely used to synthesize silver nanoclusters (AgNCs) with excellent optical properties due to their specific secondary structure. Hairpin-AgNCs have been popularly employed for sensoring applications, while no systematic study has been done about the effect of stem sequence on the fluorescence property of hairpin-AgNCs. In this presented work, the synthesizing conditions of hairpin-AgNCs were fully examined first. Then, the effect of percentage content and distribution of GC base pairs as well as stem length on the fluorescence property of hairpin-AgNCs were studied. Intriguing phenomena were observed and basic conclusions were drawn, which would be helpful to understand the hairpin-AgNCs comprehensively and instructional for the applications using hairpin-AgNC probes.

Protein-protected gold/silver alloy nanoclusters in metal-enhanced singlet oxygen generation and their correlation with photoluminescence

Photoluminescent noble metal nanoclusters (NCs, core size <2 nm) have recently emerged as a new type of photosensitizers advantageous over conventional photosensitizers due to their high singlet oxygen (¹O₂) generation efficiency, excellent photostability and water solubility, as well as good biocompatibility for photodynamic therapy and bioimaging. However, no correlation has been established between the intrinsic ¹O₂ generation and photoluminescence properties of metal NCs with their size, composition, and concentration, which is important to customize the molecule-like properties of NCs for different applications. Herein, we report a systematic study to uncover the rational design of bimetallic NCs with controllable ¹O₂ generation efficiency by tuning their compositions through spontaneous galvanic displacement reaction. A series of ultrasmall gold/silver alloy nanoclusters (AuAgNCs) were synthesized by reacting bovine serum albumin (BSA) protein-protected Ag₁₃NCs (13 Ag atoms/cluster) with varying concentrations of gold precursor at room temperature. It was found that the ¹O₂ generation efficiency of the resultant BSA-protected AuAgNCs were inversely correlated to their photoluminescence intensity. Interestingly, plasmonic gold nanoparticles (>10 nm) were also formed simultaneously by photobleaching of the BSA-AuAgNCs, leading to significant metal enhancement effect to the ¹O₂ generation rate much higher (~45 times) than that of the monometallic BSA-Ag₁₃NC. This versatile two-for-one strategy to develop next generation metal-enhanced bimetallic NC photosensitizers in one pot opens up new opportunities in designing advanced hybrid nanomaterials with complementary and/or enhanced functionalities.

Target-induced in-situ formation of fluorescent DNA-templated copper nanoparticles by a catalytic hairpin assembly: application to the determination of DNA and thrombin

A fluorometric method is described for nucleic acid signal amplification through target-induced catalytic hairpin assembly with DNA-templated copper nanoparticles (Cu NPs). The toehold-mediated self-assembly of three metastable hairpins is triggered in presence of target DNA. This leads to the formation of a three-way junction structure with protruding mononucleotides at the 3' terminus. The target DNA is released from the formed branched structure and triggers another assembly cycle. As a result, plenty of branched DNA becomes available for the synthesis of Cu NPs which have fluorescence excitation/emission maxima at 340/590 nm. At the same time, the branched structure protects the Cu NPs from digestion by exonuclease III. The unreacted hairpins are digested by exonuclease III, and this warrants a lower background signal. The method can detect ssDNA (24 nt) at low concentration (44 pM) and is selective over single-nucleotide polymorphism. On addition of an aptamer, the strategy can also be applied to the quantitation of thrombin at levels as low as 0.9 nM. Graphical abstractSchematic representation of target-induced catalytic hairpin assembly to form branched DNA template for the in situ synthesis of fluorescent Cu nanoparticles.

A Multi-Functional Silicon Nanoparticle Designed for Enhanced Osteoblast Calcification and Related Combination Therapy

Implant materials applied in bone defect commonly focus on the inducement of bone regeneration and neglect to cure complications including bacterial infection and inflammation, which may result in delayed unions or even amputation. In this study, a microporous silica nanoparticle-poly(N-isopropylacrylamide-b-(2-(dimethylamino)ethyl methacrylate) is synthesized for loading DXMS and the ECM-derived peptide (Sequence: Succinic acid-GTPGPQGIAGQRGVV) in order to enhance the osteoblast calcification and relieve related symptoms. Positively charged PDMA blocks endow the nanoparticle with the antimicrobial property. Moreover, the combination of DXMS makes it have the ability of anti-inflammation and promoting calcification formation. Furthermore, incorporation of the peptide leads to a significant improvement of mineralization and alkaline phosphatase expression in the preosteoblast. After intramuscular implantation in mice for four weeks, the results indicate the composite nanoparticle can promote ectopic bone formation. These combined properties make the composite silicon nanoparticle a promising osteogenic drug appropriate for further study in bone repair and related combination therapy.

Protein-coated dsDNA nanostars with high structural rigidity and high enzymatic and thermal stability

DNA nanotechnology creates precise shape-specific nanostructures through the self-assembly of short ssDNA oligonucleotides. One such shape, which has relevant biomedical applications due to its multivalency, is the star. However, building star-like nanostructures with a large size (>100 nm) using ssDNA is complex and challenging. This study presents a novel strategy to prepare stiff and large dsDNA nanostars by assembling duplex DNA fragments into star-shapes that are subsequently coated with a virus-inspired protein. The protein binds dsDNA and overcomes the high structural flexibility of naked dsDNA. The nanostar-like dsDNA templates with up to six arms were prepared by self-assembly of PCR-produced dsDNA fragments (211 to 722 bp) with a central DNA junction. Through gel electrophoresis and Atomic Force Microscopy it is demonstrated that single dsDNA nanostars are self-assembled and coated with the protein, and this has a large stiffening effect on the nanostar. Furthermore, the coating significantly enhances stability at high temperatures and protects nanostars against nuclease degradation for at least 10 hours. This study shows that DNA-binding proteins can be harnessed as structural "rigidifiers" of flexible branched dsDNA templates. This strategy opens a way to prepare structurally defined hybrid protein-dsDNA nanostructures that could be exploited as building blocks for novel DNA nanomaterials.

Target-Triggered Polymerization of Branched DNA Enables Enzyme-free and Fast Discrimination of Single-Base Changes

Single-base changes lead to important biological and biomedical implications; however, the discrimination of single-base changes from normal DNA always remains a grand challenge. Herein we developed a DNA recognition and amplification system based on artificial branched DNA, namely, target-triggered polymerization (TTP), to realize enzyme-free and fast discrimination of single-base changes. Branched DNA as monomers rapidly polymerized into DNA nanospheres only with the trigger of specific DNA. Our TTP system worked reliably over a wide range of conditions. Remarkably, our TTP system was capable of discriminating base-changing DNA from normal DNA, including distinguishing 1-4 nucleotide changes and positions of single base, which was attributed to the significant amplification of small differences in hybridization thermodynamics and kinetics. We further proposed a theoretical method for calculating the hybridization probability of nucleic acids, which performed highly consistent with experimental results.

Static DNA Nanostructures For Cancer Theranostics: Recent Progress In Design And Applications

Among the various nano/biomaterials used in cancer treatment, the beauty and benefits of DNA nanocomposites are outstanding. The specificity and programmability of the base pairing of DNA strands, together with their ability to conjugate with different types of functionalities have realized unsurpassed potential for the production of two- and three-dimensional nano-sized structures in any shape, size, surface chemistry and functionality. This review aims to provide an insight into the diversity of static DNA nanodevices, including DNA origami, DNA polyhedra, DNA origami arrays and bioreactors, DNA nanoswitch, DNA nanoflower, hydrogel and dendrimer as young but promising platforms for cancer theranostics. The utility and potential of the individual formats in biomedical science and especially in cancer therapy will be discussed.

Lighting Up the Gold Nanoclusters via Host-Guest Recognition for High-Efficiency Antibacterial Performance and Imaging

Au nanoclusters (Au NCs) with a unique size effect on the antibacterial performance provide a promising nanoprobe for developing an efficient nanomedicine. However, little progress has been made owing to the low quantum yield and poor stability of Au NCs. In this work, protamine (Prot) functionalized Au NCs (Prot/MTU-Au NCs) with high stability were achieved through a simple mixing with 6-methyl-2-thiouracil-capped Au NCs (MTU-Au NCs) due to the hydrogen bonding between 5-methyl-2-thiouracil (MTU) and the guanidine groups from Prot. Interestingly, a distinctly enhanced photoluminescence from Prot/MTU-Au NCs (ca. 28-fold) was observed due to the formation of rigid host-guest assemblies. We inferred that the cross-linked structure and supramolecular hydrogen bonds both contributed to the fluorescence enhancement and stability. The extra small size of the NCs and the efficient antibacterial capability from the capping shell of Prot encouraged us to probe its antibacterial performance systemically. It was found that the Prot/MTU-Au NCs with highly stable loading of positively charged antibacterial reagents were likely to penetrate into the bacteria and thus enhance the ability to kill both Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (multiple-resistant Staphylococcus aureus). The synergetic effect between the unique size and the capping layers enabled the minimal inhibitory concentration of the as-derived Prot/MTU-Au NCs reduced by ∼100-fold compared to that with individual Au nanoparticle. The antibacterial mechanism further revealed that membrane injury occurred and reactive oxygen species were generated after the incubation of the bacteria with Prot/MTU-Au NCs. Moreover, the highly luminescent fluorescence and positive surface charge of Prot/MTU-Au NCs could image the bacteria easily, which held great potential for imaging-guided antibacterial platform.

Branched DNA Architectures Produced by PCR-Based Assembly as Gene Compartments for Cell-Free Gene-Expression Reactions

The physical distance between genes plays important roles in controlling gene expression reactions in vivo. Herein, we report the design and synthesis of a branched gene architecture in which three transcription units are integrated into one framework through assembly based on the polymerase chain reaction (PCR), together with the exploitation of these constructs as "gene compartments" for cell-free gene expression reactions, probing the impact of this physical environment on gene transcription and translation. We find that the branched gene system enhances gene expression yields, in particular at low concentrations of DNA and RNA polymerase (RNAP); furthermore, in a crowded microenvironment that mimics the intracellular microenvironment, gene expression from branched genes maintains a relatively high level. We propose that the branched gene assembly forms a membrane-free gene compartment that resembles the nucleoid of prokaryotes and enables RNAP to shuttle more efficiently between neighboring transcription units, thus enhancing gene expression efficiency. Our branched DNA architecture provides a valuable platform for studying the influence of "cellular" physical environments on biochemical reactions in simplified cell-free systems.

DNA-templated silver and silver-based bimetallic clusters with remarkable and sequence-related catalytic activity toward 4-nitrophenol reduction

Illustrative pathways for the preparation of bimetallic nanoclusters using DNA-AgNC, and a schematic representation of the reduction of 4-NP to 4-AP in the presence of DNA-AgNC or bimetallic nanoclusters.

DNA Templated Metal Nanoclusters: From Emergent Properties to Unique Applications

Metal nanoclusters containing a few to several hundred atoms with sizes ranging from sub-nanometer to ∼2 nm occupy an intermediate size regime that bridges larger plasmonic nanoparticles and smaller metal complexes. With strong quantum confinement, metal nanoclusters exhibit molecule-like properties. This Account focuses on noble metal nanoclusters that are synthesized within a single stranded DNA template. Compared to other ligand protected metal nanoclusters, DNA-templated metal nanoclusters manifest intriguing physical and chemical properties that are heavily influenced by the design of DNA templates. For example, DNA-templated silver nanoclusters can show bright fluorescence, tunable emission colors, and enhanced stability by tuning the sequence of the encapsulating DNA template. DNA-templated gold nanoclusters can also serve as excellent cocatalysts, which are integratable with other biocatalysts such as enzymes. In this Account, DNA-templated silver and gold nanoclusters are selected as paradigm systems to showcase their emergent properties and unique applications. We first discuss the DNA-templated silver nanoclusters with a focus on the creation of a complementary palette of emission colors, which has potential applications for multiplex assays. The importance of the DNA template toward enhanced stability of silver nanoclusters is also demonstrated. We then introduce a special class of activable fluorescence probes that are based on the fluorescence turn-on phenomena of DNA-templated silver nanoclusters, which are named nanocluster beacons (NCBs). NCBs have distinct advantages over molecular beacons for nucleic acid detection, and their emission mechanisms are also discussed in detail. We then discuss a universal method of creating novel DNA-silver nanocluster aptamers for protein detection with high specificity. The remainder of the Account is devoted to the DNA-templated gold nanoclusters. We demonstrate that DNA-gold nanoclusters can serve as enhancers for enzymatic reduction of oxygen, which is one of the most important reactions in biofuel cells. Although DNA-templated metal nanoclusters are still in their infancy, we anticipate they will emerge as a new type of functional nanomaterial with wide applications in biology and energy science. Future research will focus on the synthesis of size selected DNA-metal nanoclusters with atomic monodispersity, structural determination of different sized DNA-metal nanoclusters, and establishment of structure-property correlations. Some long-standing mysteries, such as the origin of fluorescence and mechanism for emission color tunability, constitute the central questions regarding the photophysical properties of DNA-metal nanoclusters. On the application side, more studies are required to understand the interaction between nanocluster and biological systems. In the foreseeable future, one can expect that new biosensors, catalysts, and functional devices will be invented based on the intriguing properties of well-designed DNA-metal nanoclusters and their composites. Overall, DNA-metal nanoclusters can add additional spotlights into the highly vibrant field of ligand protected, quantum sized metal nanoclusters.

Silk fibroin-derived peptide directed silver nanoclusters for cell imaging

Fluorescent silver nanoclusters (Ag NCs) that are capable of emitting green light have been synthesized using a peptide derived from the C terminal of silk fibroin heavy chain (CSH) via a one-pot, green, and facile synthesis method. The emission was also found to be stable at the excitation wavelength and the fluorescence quantum yield of Ag NCs was measured to be 1.1%. Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) indicated the presence of a range of Ag species that correspond to Ag1, Ag2, Ag3 and Ag4. Transmission electron microscopic analyses suggested that the formed particles are uniform and well dispersive with an average diameter of 2.5 nm. The Ag NCs were successfully applied to cell imaging in murine preosteoblast MC3T3-E1 cells. Finally, Ag NCs observed by MTT exhibited distinct cytotoxicity at CSH-Ag NCs concentrations of 600 μM. Based on the concept of utilizing a functional peptide from nature, this study demonstrates a novel approach to fabricate aqueous metal nanoclusters for tracking applications in bioimaging.