Sensitive detection of miRNA based on enzyme-propelled multiple photoinduced electron transfer strategy

A method is presented that uses photoinduced electron transfer (PET) for the determination of microRNAs (miRNAs) in clinical serum samples and complicated cell samples by using a smartphone. miRNA-21 is adopted as a model analyte. A 3'-phosphorylated DNA probe containing AgNCs is synthesized and hybridized with miRNA-21. Subsequently, the probe is cleaved specifically by duplex-specific nuclease to form 3'-hydroxylated products, then extended by terminal deoxynucleotidyl transferase (TdT) with superlong G for G-quadruplex/hemin units fabrication. In this way, PET occurred between AgNCs and produced G-quadruplex/hemin units, leading to the fluorescence quenching of AgNCs. Notably, the fluorescence images can be captured and translated into digital information by smartphone, resulting in a direct quantitative determination of miRNA. As a result, our strategy for miRNA assay is achieved with a satisfactory detection limit of 1.43 pM. Interestingly, TdT-propelled G-quadruplex/hemin units as multiple electron acceptors promote the sensitivity of miRNA monitoring. Different miRNAs assays are realized by adjusting the complimentary sequences of DNA probe. These qualities not only broaden the practical application of PET-based strategy, but also provide a new insight into the nucleic acid detection. Schematic representation of AgNCs and enzyme-propelled photoinduced electron transfer strategy. It has been successfully applied for detection of miRNA by image analysis software. The method displays portability and accuracy for miRNA determination, meeting the potential for biochemical and clinical applications in resource-limited settings.

Target-triggered entropy-driven amplification system-templated silver nanoclusters for multiplexed microRNA analysis

MicroRNAs (miRNAs) are important biomarkers for the diagnosis, prognosis, and treatment of human diseases. Sensitive and selective detection of multiple miRNAs simultaneously will greatly facilitate the early and accurate diagnosis of cancers. Herein, a novel entropy-driven amplification system-templated silver nanoclusters sensing platform was developed for the multiplexed analysis of tumor-associated miRNAs. The sensing platform was constructed by coupling target-triggered entropy-driven catalysis with luminescence adjustable DNA-templated silver nanoclusters (Ag NCs). In the presence of target miRNA, the sensing platform initiates the branch migration and strand displacement of the complex, which has a six-base cytosine loop for stabilizing the luminous Ag NCs. The target is cyclically generated for new catalysis while turning off the fluorescence of Ag NCs; this is accompanied by a significantly amplified optical readout. In this study, two different complex-stabilized Ag NCs systems were proposed, the yellow-emitting Ag NCs and red-emitting Ag NCs biosensors enabled the analysis of miRNA-141 and miRNA-155 with detection limits of 6.1 pM and 8.7 pM, respectively. Impressively, owing to the excellent selectivity, flexibility, and narrow-band excitation of the platform, the multiplexed synchronous detection of miRNA-141 and miRNA-155 were achieved in buffer, biological cell lysates and human serum samples with satisfactory results. The simple, flexible, and convenient strategy provides a powerful tool for multiple biomarkers analysis and related clinical applications.

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.

A new label-free fluorescent sensor for human immunodeficiency virus detection based on exonuclease III-assisted quadratic recycling amplification and DNA-scaffolded silver nanoclusters

A label-free and sensitive fluorescence biosensing platform for human immunodeficiency virus gene (HIV-DNA) detection has been fabricated based on luminescent DNA-scaffolded silver nanoclusters (DNA/AgNCs) and autonomous exonuclease III (Exo III)-assisted recycling signal amplification. One long-chain DNA (X-DNA) molecule can hybridize with two assistant DNA (F-DNA) molecules and one HIV-DNA molecule; after Exo III digests X-DNA to liberate F-DNA and HIV-DNA. F-DNA combines with P-DNA (template of DNA/AgNCs), accordingly, P-DNA is cut and the fluorescence of the system is quenched. This assay can finish in one-step without any labelling of the DNA chain or complex construction, and the strategy is sensitive with the detection limit as low as 35 pM. At the same time, the approach exhibits good selectivity even against a single base mismatch. What's more, the method is able to monitor HIV-DNA in real human serum samples; it holds great potential for early diagnosis in gene-related diseases.

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.

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.

Label-free and ultrasensitive fluorescence detection of cocaine based on a strategy that utilizes DNA-templated silver nanoclusters and the nicking endonuclease-assisted signal amplification method

A general and reliable strategy for the detection of cocaine was proposed utilizing DNA-templated silver nanoclusters as signal indicators and the nicking endonuclease-assisted signal amplification method. This strategy can detect cocaine specifically with a detection limit as low as 2 nM by using a small volume of 5 μL.

Towards understanding of poly-guanine activated fluorescent silver nanoclusters

It has been recently reported that the fluorescence of some DNA-templated silver nanoclusters (AgNCs) can be significantly enhanced upon by hybridizing with a partially complementary DNA containing a G-rich overhang near the AgNCs. This discovery has found a number of analytical applications but many fundamental questions remain to be answered. In this work, the photostability of these activated AgNCs is reported. After adding the G-rich DNA activator, the fluorescence intensity peaks in ∼1 h and then starts to decay, where the decaying rate is much faster with light exposure. The lost fluorescence is recovered by adding NaBH4, suggesting that the bleaching is an oxidative process. Once activated, the G-rich activator can be removed while the AgNCs still maintain most of their fluorescence intensity. UV-vis spectroscopy suggests that new AgNC species are generated upon hybridization with the activator. The base sequence and length of the template DNA have also been varied, leading to different emission colors and color change after hybridization. G-rich aptamers can also serve as activators. Our results indicate that activation of the fluorescence by G-rich DNA could be a convenient method for biosensor development since the unstable NaBH4 is not required for the activation step.

Ligation-triggered fluorescent silver nanoclusters system for the detection of nicotinamide adenine dinucleotide

Herein, we demonstrate a novel silver nanocluster-based fluorescent system for the detection of nicotinamide adenine dinucleotide (NAD(+)), an important biological small molecule involved in a wide range of biological processes. A single-stranded dumbbell DNA probe was designed and used for the assay, which contained a nick in the stem, a poly-cytosine nucleotide loop close to 5' end as the template for the formation of highly fluorescent silver nanoclusters (Ag NCs) and another loop close to 3' end. Only in the presence of NAD(+), the probe was linked at 5' and 3' ends by Escherichia coli DNA ligase, which blocked the DNA polymerase-based extension reaction, ensuring the formation of fluorescent Ag NCs. This technique provided a logarithmic linear relationship in the range of 1 pM-500 nM with a detection limit of as low as 1 pM NAD(+), and exhibited high selectivity against its analogues, and was then successfully used for the detection of NAD(+) level in four kinds of cell homogenates. In addition, this new approach was conducted in an isothermal and homogeneous condition without the need of any thermal cycling, washing, and separation steps, making it very simple. Overall, this label-free protocol offers a promising alternative for the detection of NAD(+), taking advantage of specificity, sensitivity, cost-efficiency, and simplicity.

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.

Protein-directed approaches to functional nanomaterials: a case study of lysozyme

Using lysozyme as a model, protein-directed approaches to functional nanomaterials were reviewed, making rational materials design possible in the future.

Aptamer-based sensing platform using three-way DNA junction-driven strand displacement and its application in DNA logic circuit

We proposed a new three-way DNA junction-driven strand displacement mode and fabricated an aptamer-based label-free fluorescent sensing platform on the basis of this mechanism. Assembling the aptamer sequence into the three-way DNA junction makes the platform sensitive to the target of the aptamer. A label-free signal readout method, split G-quadruplex enhanced fluorescence of protoporphyrin IX (PPIX), was used to report the final signal. Here, adenosine triphosphatase (ATP) was taken as a model and detected through this approach, and DNA strand could also be detected by it. The mechanism was investigated by native polyacrylamide gel electrophoresis. Furthermore, on the basis of this molecular platform, we built a logic circuit with ATP and DNA strands as input. Aptamer played an important role in mediating the small molecule ATP to tune the DNA logic gate. Through altering the aptamer sequence, this molecular platform will be sensitive to various stimuli and applied in a wide field.

DNA-templated silver nanoclusters based label-free fluorescent molecular beacon for the detection of adenosine deaminase

A general and reliable fluorescent molecular beacon is proposed in this work utilizing DNA-templated silver nanoclusters (AgNCs). The fluorescent molecular beacon has been employed for sensitive determination of the concentration of adenosine deaminase (ADA) and its inhibition. A well-designed oligonucleotide containing three functional regions (an aptamer region for adenosine assembly, a sequence complementary to the region of the adenosine aptamer, and an inserted six bases cytosine-loop) is adopted as the core element in the strategy. The enzymatic reaction of adenosine catalyzed by ADA plays a key role as well in the regulation of the synthesis of the DNA-templated AgNCs, i.e. the signal indicator. The intensity of the fluorescence signal may thereby determine the concentration of the enzyme and its inhibitor. The detection limit of the ADA can be lowered to 0.05 UL(-1). Also, 100 fM of a known inhibitor erythro-9-(2-hydroxy-3-nonyl) adenine hydrochloride (EHNA) is enough to present distinguishable fluorescence emission. Moreover, since the fluorescent signal indicator is not required to be bound with the oligonucleotide, this fluorescent molecular beacon may integrate the advantages of both the label-free and signal-on strategies.

Detection of DNA damage by thiazole orange fluorescence probe assisted with exonuclease III

This work reports a fluorescent dye insertion approach for detection of DNA damage. The capture DNA with overhanging 3'-terminus was immobilized on silicon surface to hybridize with target DNA. The intercalation of cyanine dye of thiazole orange (TO) to the double helix structure of DNA (dsDNA) allowed intense enhancement of fluorescence signal. The DNA damage with chemicals led to poor intercalation of TO into double helix structure, resulting in the decrease of the fluorescence signal. This signal decrease could be further enhanced by exonuclease III (Exo III). With this approach, the target DNA could be detected down to 47 fM. Seven chemicals were chosen as models to monitor DNA damage. The results suggested that the present strategy could be developed to detect DNA damage, to classify the damaging mechanism with chemicals and to estimate the toxic effect of chemicals.

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.

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.

Blue emitting gold nanoclusters templated by poly-cytosine DNA at low pH and poly-adenine DNA at neutral pH

Blue fluorescent gold nanoclusters were prepared in the presence of poly-cytosine DNAs at low pH and poly-adenine at neutral pH using citrate as the reducing agent; various buffer conditions affecting the synthesis have been explored.

Silver atom and strand numbers in fluorescent and dark Ag:DNAs

We use tandem HPLC-mass spectrometry with in-line spectroscopy to identify silver atom numbers, N(Ag), of 10 to 21 in visible- to infrared-emitting Ag:DNA complexes stabilized by oligonucleotide monomers and dimers. Qualitatively different absorbance spectra from bare, same-N(Ag) silver clusters point to silver-base interactions as the origin for the color of Ag:DNAs.

DNA-mediated silver nanoclusters: synthesis, properties and applications

Fluorescent DNA-AgNCs have emerged as an alternative to standard emitters because of their unique properties: high fluorescent quantum yield, photostability, a broad pallet of colors (blue to near-IR), and the fact that their properties are easily modulated by the DNA sequence and environment. Applications as gene, ion, or small-molecule sensors have been reported.