Towards understanding of poly-guanine activated fluorescent silver nanoclusters

Interactions of coinage metal nanoclusters with low-molecular-weight biocompounds

Nowadays, coinage metal nanoclusters (NCs) are largely presented in diagnostics, bioimaging, and biocatalysis due to their high biocompatibility, chemical stability, and sensitivity to surrounding biomolecules. Silver and gold NCs are usually characterized by intense luminescence and photostability, which is in great demand in the detection of organic compounds, ions, pH, temperature, etc. The experimental synthesis of metal NCs often occurs on biopolymer templates, mostly DNA and proteins. However, this review mainly focuses on the interactions with small biomolecules (SBMs) of a molecular weight less than 1000 Da: amino acids, nucleobases, thiolates, oligopeptides, etc. Such molecules can serve as the templates for an eco-friendly facile one-pot synthesis of biocompatible luminescent NCs. The latter aspect makes NCs suitable for diagnostics and intracellular bioimaging. Another important aspect is the interaction of clusters with biomarkers, which is largely exploited by nanosensors: biomarker detection often occurs through either fluorescence emission "turn-on" or "turn-off" mechanisms. Moreover, as theoretical studies show, electronic absorption spectra and Raman spectra of the metal-organic complexes allow efficient detection of various analytes. In this regard, both theoretical and experimental studies of SBM complexes with metal NCs are in great demand. Therefore, this review aims to summarize up-to-date studies on the interaction of small biomolecules with coinage metal NCs from both theoretical and experimental viewpoints.

Detection of cancer-associated miRNA using a fluorescence switch of AgNC@NA and guanine-rich overhang sequences

DNA-templated silver nanoclusters (AgNC@DNA) are a novel type of nanomaterial with advantageous optical properties. Only a few atoms in size, the fluorescence of nanoclusters can be tuned using DNA overhangs. In this study, we explored the properties of AgNCs manufactured on a short single-stranded (dC)12 when adjacent G-rich sequences (dGN , with N = 3-15) were added. The 'red' emission of AgNC@dC12 with λMAX  = 660 nm dramatically changed upon the addition of a G-rich overhang with NG  = 15. The pattern of the emission-excitation matrix (EEM) suggested the emergence of two new emissive states at λMAX  = 575 nm and λMAX  = 710 nm. The appearance of these peaks provides an effective way to design biosensors capable of detecting specific nucleic acid sequences with low fluorescence backgrounds. We used this property to construct an NA-based switch that brings AgNC and the G overhang near one another, turning 'ON' the new fluorescence peaks only when a specific miRNA sequence is present. Next, we tested this detection switch on miR-371, which is overexpressed in prostate cancer. The results presented provide evidence that this novel fluorescent switch is both sensitive and specific with a limit of detection close to 22 picomoles of the target miR-371 molecule.

Detection of inflammatory bowel disease (IBD)-associated microRNAs by two color DNA-templated silver nanoclusters fluorescent probes

Researches demonstrated that circulating miRNAs could be used as novel diagnostic and prognostic potential markers for patients with inflammatory bowel diseases (IBD). It is of great significance in clinical to develop rapid and specific detection methods for miRNAs. Herein, we established a fluorescent probe for ulcerative colitis (UC) activity-associated two serum biomarkers (miR-23a and miR-223) simultaneous detection, which used multi-color fluorescent DNA-stabilized silver nanoclusters (DNA-AgNC) illuminated by a close guanine (G)-rich sequence as a signal transducer and two split DNA probes as recognition units. In principle, the two DNA probe sequences containing AgNC nucleation sequence and G-rich sequence respectively, formed a ternary complex when in the presence of target miRNA through base pairing, so as to induce enhancement of fluorescence emission of AgNC by shortening the distance from G-rich sequence. The combined probes for miR-23a and miR-223 detection generated increased fluorescence signals at 460 nm ex/545 nm em and at 560 nm ex/630 nm em, respectively. With this technique, we successfully quantified the two target miRNAs with high selectivity. Furthermore, the potential clinic applicability of this method was verified by testing the spiked standard miRNAs in human serum. Thus, this one-step, low-cost, and homogenous method offers a great opportunity for disease-associated multiplex miRNAs simultaneous detection.

Progress of metal nanoclusters in nucleic acid detection

The development and application of metal nanoclusters (MNCs) in nucleic acid testing in the past 10 years have been summarized. Fluorescence enhancement and red shift can occur when the G-rich sequence gets close to Ag NCs or the complementary DNA strand hybridizes with Ag NCs tail strand, which can be used to identify the nucleic acid. Ag NCs with the abasic site in DNA duplex can distinguish mutant genes such as cancer suppression gene p53. Ag NCs with auxiliary DNA can be used to detect miR-21, miR-16-5p, miR-19b-3p, and miR-141. Cu NCs/Cu NPs can recognize miRNA-155, miR-21, and miR-let-7d without auxiliary DNA. Au NCs can identify H1N1 gene fragments by fluorescence quenching caused by proximity to the G-rich sequence. Besides, Au NCs can recognize miRNA-21 and let-7a. SsDNA MNCs adsorbed on the surface of GO and CNPs oxide can be used to identify HBV and HIV gene fragments. The addition of enzymes or auxiliary amplification technologies is a popular way to improve probe sensitivity. Ag NCs combined with TAIEA has the best performance and can obtain LOD as low as aM for miRNA.

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.

Establishing empirical design rules of nucleic acid templates for the synthesis of silver nanoclusters with tunable photoluminescence and functionalities towards targeted bioimaging applications

DNA-templated silver nanoclusters (AgNCs) are an emerging class of ultrasmall (<2 nm) fluorophores with increasing popularity for bioimaging due to their facile synthesis and tunable emission color. However, design rules correlating different nucleotide sequences with the photoemission properties of AgNCs are still largely unknown, preventing the rational design of DNA templates to fine-tune the emission color, brightness and functionalities of AgNCs for any targeted applications. Herein, we report a systematic investigation to understand the empirical influences of the four basic DNA nucleotides on AgNC synthesis and their effects on photoluminescence properties. After establishing the importance of nucleotide-Ag+ binding and AgNC encapsulation within DNA tetraplex structures, we then determined the unique attributes of each individual nucleobase using different combinations of systematically varied DNA templates. Using the empirical design rules established herein, we were able to predict the photoluminescence behaviours of AgNCs templated by complex aptamer sequences with specific binding affinity to human cancer cells, and to deliberately control their emission color by rational modifications of the DNA template sequences for targeted bioimaging. Our empirical findings from this systematic experimentation can contribute towards the rational design of DNA sequences to customise the photoluminescence properties and biofunctionalities of DNA-protected AgNCs towards multicolour targeted bioimaging applications.

First Step Towards Larger DNA-Based Assemblies of Fluorescent Silver Nanoclusters: Template Design and Detailed Characterization of Optical Properties

Besides being a passive carrier of genetic information, DNA can also serve as an architecture template for the synthesis of novel fluorescent nanomaterials that are arranged in a highly organized network of functional entities such as fluorescent silver nanoclusters (AgNCs). Only a few atoms in size, the properties of AgNCs can be tuned using a variety of templating DNA sequences, overhangs, and neighboring duplex regions. In this study, we explore the properties of AgNCs manufactured on a short DNA sequence-an individual element designed for a construction of a larger DNA-based functional assembly. The effects of close proximity of the double-stranded DNA, the directionality of templating single-stranded sequence, and conformational heterogeneity of the template are presented. We observe differences between designs containing the same AgNC templating sequence-twelve consecutive cytosines, (dC)12. AgNCs synthesized on a single "basic" templating element, (dC)12, emit in "red". The addition of double-stranded DNA core, required for the larger assemblies, changes optical properties of the silver nanoclusters by adding a new population of clusters emitting in "green". A new population of "blue" emitting clusters forms only when ssDNA templating sequence is placed on the 5' end of the double-stranded core. We also compare properties of silver nanoclusters, which were incorporated into a dimeric structure-a first step towards a larger assembly.

The presence of a single-nucleotide mismatch in linker increases the fluorescence of guanine-enhanced DNA-templated Ag nanoclusters and their application for highly sensitive detection of cyanide

Fluorescence of DNA-templated silver nanoclusters can be enhanced by more than 100-fold by placing the nanoclusters in proximity to guanine-rich DNA sequences after hybridization. We found that the fluorescence of the guanine-enhanced silver nanoclusters is not increased with the guanine-rich DNA sequence closer to the silver nanoclusters. By studying the different numbers of mismatches in the linker sequences, we found that the presence of a single-nucleotide mismatch in the linker increases fluorescence more than the complementary nucleotide. Further study indicated the mismatch position of the linker sequence also affects the fluorescence of the hybridized DNA-Ag NCs. The evidence reported here indicated that the mismatch of the linker sequence affects the fluorescence enhancement of guanine-enhanced silver nanoclusters. We also found that DNA-Ag NCs is an excellent fluorescence sensor for cyanide, as cyanide effectively quenches the fluorescence of NCs at a very low concentration with high selectivity. Cyanide in the range from 0.10 μM to 0.35 μM could be linearly detected, with a detection limit of 25.6 nM.

The role of spacer sequence in modulating turn-on fluorescence of DNA-templated silver nanoclusters

Guanine activation of fluorescence in DNA templated silver nanoclusters (AgNCs) is an interesting physical phenomenon which has yet to be fully understood to date. While the individual role of cytosine and guanine has been established, there is still a knowledge gap on how the AgNC-DNA system switches from dark to bright state. Here, we present evidence on the universal role of the DNA spacer sequence in physically separating two Ag+-binding cytosine sites to maintain the dark state while holding them together for structural re-organization by the guanine-rich strand to activate the bright state. The extent of turn-on signal could be modulated by adjusting the spacer length and composition. The ATATA spacer sequence was found to have negligible dark state fluorescence and a turn-on effect of 2440-fold, which was almost five times of the highest factor reported to date.

Highly Stable and Multiemissive Silver Nanoclusters Synthesized in Situ in a DNA Hydrogel and Their Application for Hydroxyl Radical Sensing

Oligonucleotide-stabilized silver nanoclusters (AgNCs) show promising applications in bioimaging and bio-/chemo-sensing. However, their unsatisfactory photostability limits their practical applications. In this work, fluorescent AgNCs were synthesized in situ in a DNA hydrogel, consisting of cross-linked enzymatically amplified polymeric DNAs with cytosine-rich sequences in the presence of Ag⁺. The fluorescence property of the resultant AgNCs was optimized by a rational design of the DNA sequences to cover a broad spectrum with comparable green and red emissions. Under the protection of the DNA hydrogel, the AgNCs showed significantly improved photostability in an ambient oxygen environment, as well as low cytotoxicity even at a high concentration. Therefore, these properties show the rolling-circle-amplification-stabilized AgNCs to be a promising possible fluorescent probe for the detection of reactive oxygen/nitrogen species (ROS/RNS) in live cells because red-emitting species are susceptible to oxidation and consequently convert to green-emitting species. Finally, the as-prepared AgNCs were demonstrated to be a sensitive and specific probe for cellular imaging and the monitoring of ROS/RNS levels, which broadens the applications of AgNCs and provides a new tool for related biological investigations.

DNA-templated silver nanoclusters locate microRNAs in the nuclei of gastric cancer cells

Dysregulation of microRNAs (miRNAs) is correlated with cancer progression. In vitro detection methods using extracts from cell lysis cannot provide information about the spatial distribution of miRNAs. Due to the development of miRNA fluorescence in situ hybridization (FISH), increasing amounts of intracellular expression information are being obtained. However, miRNA FISH suffers from weak signals and complex steps and thus remains very challenging. Herein, a strategy based on DNA-templated silver nanoclusters (AgNCs/DNAs) and their G-rich fluorescence enhancement effect was developed for FISH detection of miRNAs in gastric cancer cells. The method combines hybridization and signal amplification into one step, which allows imaging of intracellular miRNAs immediately after hybridization. Most importantly, using the method based on our design, miR-101-3p, miR-16-5p and miR-19b-3p were found to be located in the nuclei of MGC803 cells with granulated shapes, indicating an unanticipated distribution pattern. In addition, before the final miRNA FISH, we performed an optimization of AgNCs/DNAs and their G-rich fluorescence enhancement effect; we found that the effect occurred at shorter wavelengths emitting green fluorescence, with weakened red fluorescence at longer wavelengths. However, the components involved in the FISH process impacted the fluorescence properties so greatly that the probes finally exhibited slightly strengthened red fluorescence signals. Our method enables facile visualization of miRNAs at the subcellular level, which may benefit the precise localization of miRNAs in single cells in the future.

Ratiometric Catalyzed-Assembly of NanoCluster Beacons: A Nonenzymatic Approach for Amplified DNA Detection

In this work, a novel fluorescent transformation phenomenon of oligonucleotide-encapsulated silver nanoclusters (AgNCs) was demonstrated, in which green-emissive AgNCs effectively transformed to red-emissive AgNCs when placed in close proximity to a special DNA fragment (denoted as convertor here). Taking advantage of a catalyzed-hairpin-assembly (CHA) amplification strategy, we rationally and compatibly engineered a simple and sensitive AgNC-based fluorescent signal amplification strategy through the ratiometric catalyzed-assembly (RCA) of green-emissive NanoCluster Beacon (NCB) with a convertor modified DNA hairpin to induce the template transformation circularly. The proposed ratiometric fluorescent biosensing platform based on RCA-amplified NCB (RCA-NCB) emits intense green fluorescence in the absence of target DNA and will undergo consecutively fluorescent signal transformation from green emission to red emission upon exposure to its target DNA. The ratiometric adaptation of the NCB to CHA circuit advances their general usability as biosensing platform with great improvements in detection sensitivity. By measuring the fluorescence intensity ratio of the red emission and green emission, the proposed RCA-NCB platform exhibits sensitive and accurate analytical performance toward Werner Syndrome-relevant gene, the proof-of-concept target in this work. A low detection limit down to the pM level was achieved, which is lower than most of the reported AgNC-based fluorescent DNA biosensors, making the proposed RCA-NCB biosensing strategy appealing in amplifying the ratiometric fluorescent signal for sensitive DNA detection. Moreover, our proposed RCA-NCB platform shows good recovery toward the target DNA in real human serum samples, illustrating their potential promise for clinical and imaging applications in the future.

Constructing a Robust Fluorescent DNA-Stabilized Silver Nanocluster Probe Module by Attaching a Duplex Moiety

Fluorescent DNA-templated silver nanoclusters (DNA-Ag NCs) have served as excellent luminescent probes and operation units in various applications. However, the fluorescence property of DNA-Ag NCs is very sensitive to elongation or modification of the DNA template, limiting the breadth of applications. In this work, we propose a strategy for constructing a robust fluorescent DNA-Ag NCs probe module by attaching a duplex moiety to the nanocluster-bearing sequence. The fluorescence intensity of the DNA-Ag NCs can be enhanced 90-fold upon hybridization of the elongated moiety. Adenine in the linker sequence has a further enhancing effect on the fluorescence intensity, whereas thymine has a quenching effect. The transformation from a non-fluorescent species to fluorescent nanoclusters is responsible for the fluorescence enhancement with duplex formation of the elongated moiety. We hope that this design will aid future diversification of experimental designs to facilitate more applications that are currently limited by the aforementioned problems.

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.

A label-free kissing complex-induced fluorescence sensor for DNA and RNA detection by using DNA-templated silver nanoclusters as a signal transducer

A new strategy integrate silver nanoclusters (AgNCs) and riboswitches for the expanding of the application of a kissing complexes-induced sensor (KCIS) for the assay of DNA and RNA was reported.

Nucleic-acid-programmed Ag-nanoclusters as a generic platform for visualization of latent fingerprints and exogenous substances

A nucleic acid controlled AgNC platform for simultaneous imaging and quantitative detection of substances in fingerprints.

Hairpin DNA-Templated Silver Nanoclusters as Novel Beacons in Strand Displacement Amplification for MicroRNA Detection

MicroRNA (miRNA) biomarkers display great potential for cancer diagnosis and prognosis. The development of rapid and specific methods for miRNA detection has become a hotspot. Herein, hairpin DNA-templated silver nanoclusters (AgNCs/HpDNA) were prepared and integrated into strand-displacement amplification (SDA) as a novel beacon for miRNA detection. The light-up platform was established based on guanine (G)-rich fluorescence enhancement that essentially converted the excitation/emission pair of AgNCs/HpDNAs from a shorter wavelength to a longer wavelength, and then achieved fluorescent enhancement at longer wavelength. On the basis of the validation of the method, the single and duplex detection were conducted in two plasma biomarkers (miR-16-5p and miR-19b-3p) for the diagnosis of gastric cancer. The probe (AgNCs/RED 16(7s)C) utilized for miR-16-5p detection adopted a better conformation with high specificity to recognize single-base mismatches by producing dramatically opposite signals (increase or decrease at 580 nm ex/640 nm em) while the probe (AgNCs/GRE 19b(5s)C) for miR-19b-3p generated dual signals (increase at 490 nm ex/570 nm em and decrease at 430 nm ex/530 nm em) with bright fluorescence in one reaction during the amplification, but unexpectedly was partially digested. This is for the first time to allow the generation of enhanced fluorescent AgNCs and the target recognition integrated into a single process, which offers great opportunity for specific miRNA detection in an easy and rapid way.

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.

Protein-DNA interactions: a novel approach to improve the fluorescence stability of DNA/Ag nanoclusters

Protein-DNA interactions are known to play an important role in a variety of biological processes. We have shown here that protein-DNA binding events can also be used to greatly improve the fluorescence stability of DNA-templated Ag nanoclusters (Ag NCs), which would be highly beneficial for Ag NCs in applications of biosensing/imaging.

Rational design of signal-on biosensors by using photoinduced electron transfer between Ag nanoclusters and split G-quadruplex halves–hemin complexes

Photoinduced electron transfer (PET) between DNA–Ag nanoclusters (AgNCs) and G-quadruplex halves–hemin has been used for building a new sensing platform for the signal-on detection of adenosine and RNA.