Ag K-Edge EXAFS Analysis of DNA-Templated Fluorescent Silver Nanoclusters: Insight into the Structural Origins of Emission Tuning by DNA Sequence Variations

Bacterial-responsive biodegradable silver nanoclusters composite hydrogel for infected wound therapy

Skin wounds are susceptible to bacterial infections, which hinder healing and extend recovery. Herein, we designed a silver nanoclusters (Ag NCs) composite hydrogel for infected wound treatment via bacterial enzymatic degradation and Ag release. Using biocompatible gelatine and polyethylene glycol as the main components, DNA-templated Ag NCs were covalently linked to a polymer network to obtain the final nanocomposite hydrogel. This hydrogel exhibited good compressive and tensile stiffness, bioadhesion and water absorption. The overexpressed bacterial enzymes protease and DNase in the infected wound were hydrolysed by the gel matrix, subsequently releasing antibacterial Ag ions. In vitro experimental results proved that the hydrogel demonstrated excellent bactericidal effect on Staphylococcus aureus and Escherichia coli, which are commonly implicated in clinical wound infections. Animal experiments revealed that the hydrogel considerably promoted cell proliferation and wound healing with less inflammatory responses. Thus, these results demonstrate strategies for bacterial enzyme-responsive Ag release for infected wound healing, facilitating further development of intelligent bandages.

Fluorescent DNA-Silver nanoclusters in food safety detection: From synthesis to application

In recent years, the conventional preparation of silver nanoclusters (AgNCs) has attracted much attention due to their ultra-small size, tunable fluorescence, easy-to-engineer, as well as biocompatible material. Moreover, its great affinity towards cytosine bases on single-stranded DNA has led to the construction of biosensors, especially aptamers, for a broad variety of applications in food safety and environmental protection. In past years, numerous researchers paid attention to the construction of AgNCs aptasensor. Therefore, this review will be an effort to summarize the synthetic strategy along with the influences of factors on synthesis, categorize the sensing mechanism of aptamer-functionalized AgNCs biosensors, as well as their specific applications in food safety detection including heavy metal, toxin, and foodborne pathogenic bacteria. Furthermore, a brief conclusion and outlook regarding the prospects and challenges of their applications in food safety were drawn in line with the developments in DNA-AgNCs.

Structure and luminescence of DNA-templated silver clusters

DNA serves as a versatile template for few-atom silver clusters and their organized self-assembly. These clusters possess unique structural and photophysical properties that are programmed into the DNA template sequence, resulting in a rich palette of fluorophores which hold promise as chemical and biomolecular sensors, biolabels, and nanophotonic elements. Here, we review recent advances in the fundamental understanding of DNA-templated silver clusters (Ag N -DNAs), including the role played by the silver-mediated DNA complexes which are synthetic precursors to Ag N -DNAs, structure-property relations of Ag N -DNAs, and the excited state dynamics leading to fluorescence in these clusters. We also summarize the current understanding of how DNA sequence selects the properties of Ag N -DNAs and how sequence can be harnessed for informed design and for ordered multi-cluster assembly. To catalyze future research, we end with a discussion of several opportunities and challenges, both fundamental and applied, for the Ag N -DNA research community. A comprehensive fundamental understanding of this class of metal cluster fluorophores can provide the basis for rational design and for advancement of their applications in fluorescence-based sensing, biosciences, nanophotonics, and catalysis.

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.

High accuracy determination of photoelectric cross sections, X-ray absorption fine structure and nanostructure analysis of zinc selenide using the X-ray extended range technique

Measurements of mass attenuation coefficients and X-ray absorption fine structure (XAFS) of zinc selenide (ZnSe) are reported to accuracies typically better than 0.13%. The high accuracy of the results presented here is due to our successful implementation of the X-ray extended range technique, a relatively new methodology, which can be set up on most synchrotron X-ray beamlines. 561 attenuation coefficients were recorded in the energy range 6.8-15 keV with measurements concentrated at the zinc and selenium pre-edge, near-edge and fine-structure absorption edge regions. This accuracy yielded detailed nanostructural analysis of room-temperature ZnSe with full uncertainty propagation. Bond lengths, accurate to 0.003 Å to 0.009 Å, or 0.1% to 0.3%, are plausible and physical. Small variation from a crystalline structure suggests local dynamic motion beyond that of a standard crystal lattice, noting that XAFS is sensitive to dynamic correlated motion. The results obtained in this work are the most accurate to date with comparisons with theoretically determined values of the attenuation showing discrepancies from literature theory of up to 4%, motivating further investigation into the origin of such discrepancies.

Noncanonical Head-to-Head Hairpin DNA Dimerization Is Essential for the Synthesis of Orange Emissive Silver Nanoclusters

DNA secondary structures, such as dimers and hairpins, are important for the synthesis of DNA template-embedded silver nanoclusters (DNA/AgNCs). However, the arrangement of AgNCs within a given DNA template and how the AgNC influences the secondary structure of the DNA template are still unclear. Here, we introduce a noncanonical head-to-head hairpin DNA nanostructure that is driven by orange-emissive AgNCs. Through detailed in-gel analysis, sugar backbone switching, inductively coupled plasma mass spectrometry, small-angle X-ray scattering, and small angle neutron scattering, we show that the orange-emissive AgNCs mediate cytosine-Ag-cytosine bridging between two six-cytosine loop (6C-loop) hairpin DNA templates. Unlike green, red, or far-red emissive AgNCs, which are embedded inside a hairpin and duplex DNA template, the orange-emissive AgNCs are localized on the interface between the two 6C-loop hairpin DNA templates, thereby linking them. Moreover, we found that deoxyribose in the backbone of the 6C-loop at the third and fourth cytosines is crucial for the formation of the orange-emissive AgNCs and the head-to-head hairpin DNA structure. Taken together, we suggest that the specific wavelength of AgNCs fluorescence is determined by the mutual interaction between the secondary or tertiary structures of DNA- and AgNC-mediated intermolecular DNA cross-linking.

Footprints of Nanoscale DNA-Silver Cluster Chromophores via Activated-Electron Photodetachment Mass Spectrometry

DNA-templated silver clusters (AgC) are fluorescent probes and biosensors whose electronic spectra can be tuned by their DNA hosts. However, the underlying rules that relate DNA sequence and structure to DNA-AgC fluorescence and photophysics are largely empirical. Here, we employ 193 nm activated electron photodetachment (a-EPD) mass spectrometry as a hybrid MS³ approach to gain structural insight into these nanoscale chromophores. Two DNA-AgC systems are investigated with a 20 nt single-stranded DNA (ssDNA) and a 28 nt hybrid hairpin/single-stranded DNA (hpDNA). Both oligonucleotides template Ag₁₀ clusters, but the two complexes are distinct chromophores: the former has a violet absorption at 400 nm with no observable emission, while the latter has a blue-green absorption at 490 nm with strong green emission at 550 nm. Via identification of both apo and holo (AgC-containing) sequence ions generated upon a-EPD and mapping areas of sequence dropout, specific DNA regions that encapsulate the AgC are assigned and attributed to the coordination with the DNA nucleobases. These a-EPD footprints are distinct for the two complexes. The ssDNA contacts the cluster via four nucleobases (CCTT) in the central region of the strand, whereas the hpDNA coordinates the cluster via 13 nucleobases (TTCCCGCCTTTTG) in the double-stranded region of the hairpin. This difference is consistent with prior X-ray scattering spectra and suggests that the clusters can adapt to different DNA hosts. More importantly, the a-EPD footprints directly identify the nucleobases that are in direct contact with the AgC. As these contacting nucleobases can tune the electronic structures of the Ag core and protect the AgC from collisional quenching in solution, understanding the DNA-silver contacts within these complexes will facilitate future biosensor designs.

Crystal structure of a NIR-Emitting DNA-Stabilized Ag16 Nanocluster

DNA has been used as a scaffold to stabilize small, atomically monodisperse silver nanoclusters, which have attracted attention due to their intriguing photophysical properties. Herein, we describe the X-ray crystal structure of a DNA-encapsulated, near-infrared emitting Ag₁₆ nanocluster (DNA-Ag₁₆ NC). The asymmetric unit of the crystal contains two DNA-Ag₁₆ NCs and the crystal packing between the DNA-Ag₁₆ NCs is promoted by several interactions, such as two silver-mediated base pairs between 3'-terminal adenines, two phosphate-Ca²⁺ -phosphate interactions, and π-stacking between two neighboring thymines. Each Ag₁₆ NC is confined by two DNA decamers that take on a horse-shoe-like conformation and is almost fully shielded from the solvent environment. This structural insight will aid in the determination of the structure/photophysical property relationship for this class of emitters and opens up new research opportunities in fluorescence imaging and sensing using noble-metal clusters.

Highly sensitive detection of the human papillomavirus E6 protein by DNA-protected silver nanoclusters and the intrinsic mechanism

The present study not only supplies a good approach for the early diagnosis of HPV-related cancer but also enriches the biological application of AgNCs–dsDNA.

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.

Origin of the bright photoluminescence of few-atom silver clusters confined in LTA zeolites

Silver (Ag) clusters confined in matrices possess remarkable luminescence properties, but little is known about their structural and electronic properties. We characterized the bright green luminescence of Ag clusters confined in partially exchanged Ag–Linde Type A (LTA) zeolites by means of a combination of x-ray excited optical luminescence-extended x-ray absorption fine structure, time-dependent–density functional theory calculations, and time-resolved spectroscopy. A mixture of tetrahedral Ag4(H2O)x2+(x= 2 andx= 4) clusters occupies the center of a fraction of the sodalite cages. Their optical properties originate from a confined two-electron superatom quantum system with hybridized Ag and water O orbitals delocalized over the cluster. Upon excitation, one electron of the s-type highest occupied molecular orbital is promoted to the p-type lowest unoccupied molecular orbitals and relaxes through enhanced intersystem crossing into long-lived triplet states.

Excited-State Relaxation and Förster Resonance Energy Transfer in an Organic Fluorophore/Silver Nanocluster Dyad

A single-stranded DNA-based (ssDNA) dyad was constructed comprising 15 silver atoms stabilized by a ssDNA scaffold (DNA-AgNC) and an Alexa 546 fluorophore bound to the 5' end. The Alexa 546 was chosen to function as a Förster resonance energy transfer (FRET) donor for the AgNC. Time-correlated single photon counting (TCSPC) experiments allowed unraveling the excited-state relaxation processes of the purified DNA-AgNC-only system. The TCSPC results revealed slow relaxation dynamics and a red shift of the emission spectrum during the excited-state lifetime. The results from the model systems were needed to understand the more complicated decay pathways present in the collected high-performance liquid chromatography fraction, which contained the dyad (37% of the emissive population). In the dyad system, the FRET efficiency between donor and acceptor was determined to be 94% using TCSPC, yielding a center-to-center distance of 4.6 nm. To date, only limited structural information on DNA-AgNCs is available and the use of TCSPC and FRET can provide information on the center-to-center distance between chromophores and provide positional information in nanostructures composed of AgNCs.

DNA-templated silver nanoclusters: structural correlation and fluorescence modulation

12 years after the introduction of DNA-templated silver nanoclusters (DNA-AgNCs), exciting progress has been made and yet we are still in the midst of trying to fully understand this nanomaterial. The prominent excellence of DNA-AgNCs is undoubtedly its modulatable emission property, of which how variation in DNA templates causes emission tuning remains elusive. Based on the up-to-date DNA-AgNCs, we aim to establish the correlation between the structure/sequence of DNA templates and emission behaviour of AgNCs. Herein, we systematically present a wide-range of DNA-AgNCs based on the structural complexity of the DNA templates, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), triple-stranded DNA (tsDNA) and DNA nanostructures. For each DNA category, we discuss the emission property, quantum yield and synthesis condition of the respective AgNCs, before cross-comparing the impact of different DNA scaffolds on the properties of AgNCs. A future outlook for this area is given as a conclusion. By putting the information together, this review may shed new light on understanding DNA-AgNCs while we are expecting continuous breakthroughs in this field.

Tuning the energetics and tailoring the optical properties of silver clusters confined in zeolites

The integration of metal atoms and clusters in well-defined dielectric cavities is a powerful strategy to impart new properties to them that depend on the size and geometry of the confined space as well as on metal-host electrostatic interactions. Here, we unravel the dependence of the electronic properties of metal clusters on space confinement by studying the ionization potential of silver clusters embedded in four different zeolite environments over a range of silver concentrations. Extensive characterization reveals a strong influence of silver loading and host environment on the cluster ionization potential, which is also correlated to the cluster's optical and structural properties. Through fine-tuning of the zeolite host environment, we demonstrate photoluminescence quantum yields approaching unity. This work extends our understanding of structure-property relationships of small metal clusters and applies this understanding to develop highly photoluminescent materials with potential applications in optoelectronics and bioimaging.

Enzymatic polymerization of poly(thymine) for the synthesis of copper nanoparticles with tunable size and their application in enzyme sensing

A bottom-up strategy was developed for the enzyme mediated synthesis of Cu nanoparticles, which showed good sensing performance.

Additive and enhanced fluorescence effects of hairpin DNA template-based copper nanoparticles and their application for the detection of NAD(.)

DNA is an excellent molecular scaffold for the preparation of copper nanoparticles (CuNPs). However, screening and designing an efficient template for the formation of fluorescent CuNPs remains a challenge. Herein, we synthesized CuNPs using a novel hairpin DNA template with a poly T loop and a random double strand stem which performs efficient in the formation of fluorescent CuNPs. Besides, the additive and enhanced effects between the loop and stem sequences on the fluorescence of induced CuNPs was first proposed and investigated. On comparing different sequences, we found that both the circular poly T sequence on the loop region and the stem sequence play important roles in this fluorescence enhancement effect. A label-free analytical system for the quantitative detection of NAD(+) was designed, demonstrating excellent sensitivity. Based on our design concept proposed herein, any random double-stranded DNA can be used for the design of efficient templates for the formation of fluorescent CuNPs in biochemical sensing.

Gold nanocluster formation using morpholino oligomer as template and assembly agent within hybrid bio-nanomaterials

A novel 6-atom gold nanocluster is templated by a phosphorodiamidate oligomer and binds to a P,N,N pocket of the ligand backbone, as opposed to the peripheral nucleobases.

Hexaphenylbenzene-Stabilized Luminescent Silver Nanoclusters: A Potential Catalytic System for the Cycloaddition of Terminal Alkynes with Isocyanides

A hexaphenylbenzene (HPB)-based derivative bearing thiol groups has been designed and synthesized that undergoes aggregation-induced emission enhancement in mixed aqueous media to form rodlike fluorescent aggregates. These rodlike aggregates behave as a "not quenched" probe for the detection of silver ions and further act as reactors and stabilizers for reducing-agent-free preparation of blue luminescent silver nanoclusters at room temperature. The utilization of fluorescent supramolecular aggregates for the preparation of Ag NCs in mixed aqueous media is unprecedented in the literature. Moreover, the wet chemical method that we are reporting in the present paper for the preparation of luminescent silver nanoclusters is better than the other methods reported in the literature. Further, these in situ generated Ag NCs showed exceptional catalytic activity in the preparation of pyrroles involving cocyclization of isocyanides and terminal alkynes. Interestingly, the catalytic efficiency of in situ generated Ag NCs was found to be better than the other catalytic systems reported in the literature.

DNA-templated fluorescent gold nanoclusters reduced by Good’s buffer: from blue-emitting seeds to red and near infrared emitters

DNA-templated fluorescent gold nanoclusters (AuNCs) have been recently prepared showing higher photostability than the silver counterpart. In this work, we examined the effect of pH, DNA length, DNA sequence, and reducing agent. Citrate, HEPES, and MES produce blue emitters, glucose and NaBH4 cannot produce fluorescent AuNCs, while ascorbate shows blue emission even in the absence of DNA. This is the first report of using Good’s buffer for making fluorescent AuNCs. Dimethylamine borane (DMAB) produces red emitters. Poly-C DNA produces AuNCs only at low pH and each DNA chain can only bind to a few gold atoms, regardless of the DNA length. Otherwise, large nonfluorescent gold nanoparticles (AuNPs) are formed. Each poly-A DNA might template a few independent AuNCs. The blue emitters can be further reduced to form red emitters by adding DMAB. The emission color is mainly determined by the type of reducing agent instead of DNA sequence.

Ligand-assisted etching: the stability of silver nanoparticles and the generation of luminescent silver nanodots

The etching mechanism of silver nanoparticles was investigated. Though a strong binding agent to silver and an oxidising agent synergistically etch the nanoparticles, the balanced etching power has to be optimized to generate luminescent silver nanodots. This indicates that active centres facilitate the formation of nanodots.

DNA-Protected Silver Clusters for Nanophotonics

DNA-protected silver clusters (Ag_N-DNA) possess unique fluorescence properties that depend on the specific DNA template that stabilizes the cluster. They exhibit peak emission wavelengths that range across the visible and near-IR spectrum. This wide color palette, combined with low toxicity, high fluorescence quantum yields of some clusters, low synthesis costs, small cluster sizes and compatibility with DNA are enabling many applications that employ Ag_N-DNA. Here we review what is known about the underlying composition and structure of Ag_N-DNA, and how these relate to the optical properties of these fascinating, hybrid biomolecule-metal cluster nanomaterials. We place Ag_N-DNA in the general context of ligand-stabilized metal clusters and compare their properties to those of other noble metal clusters stabilized by small molecule ligands. The methods used to isolate pure Ag_N-DNA for analysis of composition and for studies of solution and single-emitter optical properties are discussed. We give a brief overview of structurally sensitive chiroptical studies, both theoretical and experimental, and review experiments on bringing silver clusters of distinct size and color into nanoscale DNA assemblies. Progress towards using DNA scaffolds to assemble multi-cluster arrays is also reviewed.

Modeling of structural, energetic, and dynamic properties of few-atom silver clusters embedded in polynucleotide strands by using molecular dynamics

This work concerns the study of the structural, energetic, and dynamic properties of fluorescent systems composed of silver clusters stabilized by polynucleotide strands. To do so, classical interaction potentials relative to silver, neutral and cationic, were introduced in the AMBER force field. Molecular dynamics simulations allowed analysis of the nature and force of the interactions between the various parts of the nucleic oligomers and the silver clusters. Conformational analyses were necessary to explore the flexibility of the supramolecular assemblies, specifically by radial distribution functions and Ramachandran-type maps.

A complementary palette of NanoCluster Beacons

NanoCluster Beacons (NCBs), which use few-atom DNA-templated silver clusters as reporters, are a type of activatable molecular probes that are low-cost and easy to prepare. While NCBs provide a high fluorescence enhancement ratio upon activation, their activation colors are currently limited. Here we report a simple method to design NCBs with complementary emission colors, creating a set of multicolor probes for homogeneous, separation-free detection. By systematically altering the position and the number of cytosines in the cluster-nucleation sequence, we have tuned the activation colors of NCBs to green (C8-8, 460 nm/555 nm); yellow (C5-5, 525 nm/585 nm); red (C3-4, 580 nm/635 nm); and near-infrared (C3-3, 645 nm/695 nm). At the same NCB concentration, the activated yellow NCB (C5-5) was found to be 1.3 times brighter than the traditional red NCB (C3-4). Three of the four colors (green, yellow, and red) were relatively spectrally pure. We also found that subtle changes in the linker sequence (down to the single-nucleotide level) could significantly alter the emission spectrum pattern of an NCB. When the length of linker sequences was increased, the emission peaks were found to migrate in a periodic fashion, suggesting short-range interactions between silver clusters and nucleobases. Size exclusion chromatography results indicated that the activated NCBs are more compact than their native duplex forms. Our findings demonstrate the unique photophysical properties and environmental sensitivities of few-atom DNA-templated silver clusters, which are not seen before in common organic dyes or luminescent crystals.

Chiral electronic transitions in fluorescent silver clusters stabilized by DNA

Fluorescent, DNA-stabilized silver clusters are receiving much attention for sequence-selected colors and high quantum yields. However, limited knowledge of cluster structure is constraining further development of these "AgN-DNA" nanomaterials. We report the structurally sensitive, chiroptical activity of four pure AgN-DNA with wide ranging colors. Ubiquitous features in circular dichroism (CD) spectra include a positive dichroic peak overlying the lowest energy absorbance peak and highly anisotropic, negative dichroic peaks at energies well below DNA transitions. Quantum chemical calculations for bare chains of silver atoms with nonplanar curvature also exhibit these striking features, indicating electron flow along a chiral, filamentary metallic path as the origin for low-energy AgN-DNA transitions. Relative to the bare DNA, marked UV changes in CD spectra of AgN-DNA and silver cation-DNA solutions indicate that ionic silver content constrains nucleobase conformation. Changes in solvent composition alone can reorganize cluster structure, reconfiguring chiroptical properties and fluorescence.

Role of anion polarizability in fluorescence sensitization of DNA-templated silver nanoclusters

Fluorescent silver nanoclusters (Ag NCs) as novel fluorophores have received much attention because of their high brightness, good photostability and widely tunable emissions from the visible to the near-infrared range as a result of their size and existing environment. However, efforts are still needed to find the factors that tune the emission of Ag NCs. In this work, Ag NCs that were size-selectively grown on DNA were used to investigate the effect of the electronic properties of coordinating ligands. Halogen anions were used as the paradigm because of their periodicity in element properties. We found that addition of halogen anions did not alter the emission wavelength of Ag NCs, but the fluorescence intensity showed an initial increase at low concentrations of Cl(-), Br(-) and I(-) followed by a gradual decrease at high concentrations. No increase in fluorescence was observed for F(-) at either low or high concentration. Such specific halogen-anion sensitization of the fluorescence of Ag NCs suggests that the binding strength/manner and dipole polarizability of these anions synergistically tune the emission behavior of Ag NCs. Less fluorescence sensitization occurred for the anion having high enough polarizability to form a covalent bond with Ag NCs. The anion polarizability-sensitized fluorescence indicates the role of anion electronic properties in tuning the emission behavior of Ag NCs, which should be seriously considered in designing Ag NC-based sensors and devices.

Bioinspired greigite magnetic nanocrystals: chemical synthesis and biomedicine applications

Large scale greigite with uniform dimensions has stimulated significant demands for applications such as hyperthermia, photovoltaics, medicine and cell separation, etc. However, the inhomogeneity and hydrophobicity for most of the as prepared greigite crystals has limited their applications in biomedicine. Herein, we report a green chemical method utilizing β-cyclodextrin (β-CD) and polyethylene glycol (PEG) to synthesize bioinspired greigite (Fe₃S₄) magnetic nanocrystals (GMNCs) with similar structure and magnetic property of magnetosome in a large scale. β-CD and PEG is responsible to control the crystal phase and morphology, as well as to bound onto the surface of nanocrystals and form polymer layers. The GMNCs exhibit a transverse relaxivity of 94.8 mM⁻¹s⁻¹ which is as high as iron oxide nanocrystals, and an entrapment efficiency of 58.7% for magnetic guided delivery of chemotherapeutic drug doxorubicin. Moreover, enhanced chemotherapeutic treatment of mice tumor was obtained via intravenous injection of doxorubicin loaded GMNCs.

A silver cluster-DNA equilibrium

DNA encapsulates silver clusters, and these hybrid nanomaterials form molecular sensors. We discuss a silver cluster-oligonucleotide sensor with four characteristics. First, a specific reporting cluster forms within a single-stranded DNA. This template uses the 5' cluster domain CCCCAACTCCTT with different 3' recognition sites for complementary oligonucleotides. The modular composite strand exclusively forms a cluster with λmax = 400 nm and with low emission. Conjugates were chromatographically purified, and their elemental analysis measured a cluster adduct with ∼11 silver atoms. Second, hybridization transforms the cluster. Size exclusion chromatography shows that the 3' recognition sites of the single-stranded conjugates hybridize with their complements. This secondary structural change both shifts cluster absorption from 400 to 490 nm and develops emission at 550 nm. Third, cluster size remains intact. Like their violet predecessors, purified blue-green clusters have ∼11 silver atoms. Cluster integrity is further supported by extracting the complement from the blue-green conjugate and reversing the spectral changes. Fourth, the cluster transformation is an equilibrium. Complementary strands generate an isosbestic point and thus directly link single-stranded hosts for the violet cluster and their hybridized analogs for the blue-green cluster. This equilibrium shifts with temperature. A van't Hoff analysis shows that longer and more stable duplexes favor the blue-green cluster. However, hybridized cluster hosts are less stable than their native DNA counterparts, and stability further degrades when short complements expose nucleobases within S1-S2. Duplex instability suggests that unpaired nucleobases coordinate the violet cluster and favor the single-stranded sensor. A balance between innate hybridization and exogenous folding highlights a distinct feature of silver clusters for sensing: they are both chromophoric reporters and ligands that modulate analyte-sensor interactions.

DNA-templated Ag nanoclusters as fluorescent probes for sensing and intracellular imaging of hydroxyl radicals

We have developed a simple, rapid and label-free sensor for the essential biological OH radicals based on the fluorescence quenching of DNA-templated Ag nanoclusters (DNA-Ag NCs). The OH radicals generated from the Fenton reagent attack and cleave the DNA template, which disturbs the microenvironments around Ag NCs, resulting in spontaneous aggregation due to the lack of stabilization and further the quenching of the Ag NCs fluorescence. These changes in fluorescence intensity allow sensing of OH radicals with good sensitivity and selectivity under optimal conditions. The sensor can be also applied for quantifying the radical scavenging action of antioxidants. Various characterizations including absorption spectra, fluorescence lifetimes, light scattering (LS) spectra, transmission electron microscopy (TEM), dark field light scattering imaging, and circular dichroism (CD) spectrometry have been employed to illustrate the proposed sensing mechanism. Further investigations demonstrate that the fluorescent probe could penetrate into intact cell membranes to selectively detect intracellular OH radicals induced by the phorbol myristate acetate (PMA) stimulation. These advantageous characteristics make the fluorescent DNA-Ag NCs potentially useful as a new candidate to monitor OH in broad biosystems.

Fluorescent silver nanoclusters as DNA probes

Fluorescent silver nanoclusters (few atoms, quantum sized) have attracted much attention as promising substitutes for conventional fluorophores. Due to their unique environmental sensitivities, new fluorescent probes have been developed based on silver nanoclusters for the sensitive and specific detection of DNA. In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing.

Evidence for rod-shaped DNA-stabilized silver nanocluster emitters

Fluorescent DNA-stabilized silver nanoclusters contain both cationic and neutral silver atoms. The absorbance spectra of compositionally pure solutions follow the trend expected for rod-shaped silver clusters, consistent with the polarized emission measured from individual nanoclusters. The data suggest a rod-like assembly of silver atoms, with silver cations mediating attachment to the bases.

Correlation of photobleaching, oxidation and metal induced fluorescence quenching of DNA-templated silver nanoclusters

Few-atom noble metal nanoclusters have attracted a lot of interest due to their potential applications in biosensor development, imaging and catalysis. DNA-templated silver nanoclusters (AgNCs) are of particular interest as different emission colors can be obtained by changing the DNA sequence. A popular analytical application is fluorescence quenching by Hg(2+), where d(10)-d(10) metallophilic interaction has often been proposed for associating Hg(2+) with nanoclusters. However, it cannot explain the lack of response to other d(10) ions such as Zn(2+) and Cd(2+). In our effort to elucidate the quenching mechanism, we studied a total of eight AgNCs prepared by different hairpin DNA sequences; they showed different sensitivity to Hg(2+), and DNA with a larger cytosine loop size produced more sensitive AgNCs. In all the cases, samples strongly quenched by Hg(2+) were also more easily photobleached. Light of shorter wavelengths bleached AgNCs more potently, and photobleached samples can be recovered by NaBH4. Strong fluorescence quenching was also observed with high redox potential metal ions such as Ag(+), Au(3+), Cu(2+) and Hg(2+), but not with low redox potential ions. Such metal induced quenching cannot be recovered by NaBH4. Electronic absorption and mass spectrometry studies offered further insights into the oxidation reaction. Our results correlate many important experimental observations and will fuel the further growth of this field.

DNA-Templated Molecular Silver Fluorophores

Conductive and plasmon-supporting noble metals exhibit an especially wide range of size-dependent properties, with discrete electronic levels, strong optical absorption, and efficient radiative relaxation dominating optical behavior at the ~10-atom cluster scale. In this Perspective, we describe the formation and stabilization of silver clusters using DNA templates and highlight the distinct spectroscopic and photophysical properties of the resulting hybrid fluorophores. Strong visible to near-IR emission from DNA-encapsulated silver clusters ranging in size from 5-11 atoms has been produced and characterized. Importantly, this strong Ag cluster fluorescence can be directly modulated and selectively recovered by optically controlling the dark state residence, even when faced with an overwhelming background. The strength and sequence sensitivity of the oligonucleotide-Ag interaction suggests strategies for fine tuning and stabilizing cluster-based emitters in a host of sensing and biolabeling applications that would benefit from brighter, more photostable, and quantifiable emitters in high background environments.

Silver clusters as both chromophoric reporters and DNA ligands

Molecular silver clusters conjugated with DNA act as analyte sensors. Our studies evaluate a type of cluster-laden DNA strand whose structure and silver stoichiometry change with hybridization. The sensor strand integrates two functions: the 3' region binds target DNA strands through base recognition while the 5' sequence C(3)AC(3)AC(3)TC(3)A favors formation of a near-infrared absorbing and emitting cluster. This precursor form exclusively harbors an ∼11 silver atom cluster that absorbs at 400 nm and that condenses its single-stranded host. The 3' recognition site associates with a complementary target strand, thereby effecting a 330 nm red-shift in cluster absorption and a background-limited recovery of cluster emission at 790 nm. One factor underlying these changes is sensor unfolding and aggregation. Variations in salt and oligonucleotide concentrations control cluster development by influencing DNA association. Structural studies using fluorescence anisotropy, fluorescence correlation spectroscopy, and size exclusion chromatography show that the sensor-cluster conjugate opens and subsequently dimerizes with hybridization. A second factor contributing to the spectral and photophysical changes is cluster transformation. Empirical silver stoichiometries are preserved through hybridization, so hybridized, dimeric near-infrared conjugates host twice the amount of silver in relation to their violet absorbing predecessors. These DNA structure and net silver stoichiometry alterations provide insight into how DNA-silver conjugates recognize analytes.

Performance and status of beamline BL8 at SLRI for X-ray absorption spectroscopy

Beamline BL8 of the Synchrotron Light Research Institute (Thailand) is routinely operated for X-ray absorption spectroscopy (XAS) in an intermediate photon energy range (1.25-10 keV). The photon energy is scanned by using a double-crystal monochromator, the crystal pair of which can be interchanged among KTP(011), InSb(111), Si(111) and Ge(220). The experimental set-up conveniently facilitates XAS measurements in transmission and fluorescence-yield modes at several K-edges of elements ranging from magnesium to zinc. Instrumentation and specification of the beamline and the XAS station are described, together with the determination of the available photon flux [0.1-6 × 10(10) photon s(-1) (100 mA)(-1)], energy resolution (1-5 × 10(-4)) and stability of photon energy calibration (0.07 eV), representing the beamline performance. Data quality and accuracy of XANES and EXAFS measured at BL8 are compared with those of other well established beamlines. A noted distinction of BL8 is its relatively high sensitivity for studying phosphorous, sulfur and chlorine in diluted systems and its maximum beam size of 14 mm (width) × 1 mm (height), which is suitable for bulk characterization.

Base-stacking-determined fluorescence emission of DNA abasic site-templated silver nanoclusters

DNA-templated silver nanoclusters (Ag NCs) are emerging sets of fluorophores that are widely applicable because of high brightness, good photostability, and visible to near-infrared emissions tunable using the DNA sequence and length to change the NC size. We find that fluorescent Ag NCs can be size-selectively grown at DNA abasic sites (AP site) using a constrained duplex environment opposed by a cytosine and flanked by two guanines. The size of the AP site-grown Ag NCs is not affected by the increasing Ag(+) concentration. A Job's plot analysis shows that Ag(2) NCs are the species responsible for the observed emissions. Although varying the DNA sequence one base away from the AP site (i.e., the Ag NC growth site) does not alter the size of the fluorescent Ag NCs, the emissions of the formed Ag NCs are still gradually red shifted as the sequence changes from thymine (T) to cytosine (C), adenine (A), and guanine (G). Furthermore, this emission shift is strongly dependent on the base-stacking direction of the 3'-side sequence of the 5'-G stack exactly flanking the AP site, which exhibits a larger emission alteration than altering the 5'-side sequence of the 3'-G stack flanking the AP site on the other side of the site. The excited-state lifetimes of the Ag NCs are inversely proportional to the singlet energies (ΔE(0,0)) of the Ag NCs relative to their ground state and of the vertical ionization potentials of the guanines directly flanking the AP site as determined by the base stacking. All of these results support the conclusion that the Ag NC excited state becomes more stable by interacting with a guanine base because of the larger electronic dipole moment that can be modified by the stacked sequences. Additionally, the size of the formed Ag NCs seems to be dependent on the consecutive AP site number. Thus, the AP site design in this work provides an easy way to shed light on the role of DNA base stacking in the optical properties of Ag NCs.