DNA-Ag NCs Research Articles

A Fluorescence Enhancement Sensor Based on Silver Nanoclusters Protected by Rich-G-DNA for ATP Detection.

In this study, a turn-on fluorescence sensor for the detection of adenosine 5'-triphosphate (ATP) was developed and tested using ATP-DNA2-Ag NCs. The results showed that the fluorescence of ATP-DNA2-Ag NCs was significantly enhanced with the addition of ATP. The fluorescence enhancement was a result of the specific binding activity of the ATP aptamer and ATP, which caused G-rich sequences to approach the dark DNA-Ag NCs, owing to the alteration in ATP aptamer conformation. The proposed sensor demonstrated a good linear range of 18-42 mM and a limit of detection (LOD) of 2.8 μM. The sensor's features include sensitivity, selectivity, and simple operation. In addition, the proposed sensor successfully measured ATP in 100-fold diluted fetal bovine serum.

A highly cost-effective and sensitive biosensing platform: Fuel-propelled DNA nanomachines modulate fluorescence switching of DNA silver nanoclusters

It is of great significance to develop a low-cost, simple but highly sensitive fluorescence sensing platform for low-abundance molecule detection. However, traditional organic fluorophore labeling often requires expensive and sophisticated synthesis, making it difficult to use in resource-limited areas. Besides, the traditional “one-to-one” detection mechanism presents an obstacle to sensitive detection of low-level molecules, because one target only triggers one signal. To tackle these predicaments, in this work, a brightly red-emissive three-stranded DNA stabilized silver nanocluster (Ag NC) has been successfully synthesized. However, the fluorescence emission of Ag NCs can be darkened when it is in a loose single-stranded DNA. Building on this finding, we elaborately engineer a highly cost-effective and sensitive biosensing platform, which exploits a target-triggered and fuel-driven DNA nanomachine to precisely manipulate the structural transformation of Ag NCs from the rigid three-stranded DNA structures to the flexible single-stranded DNA, accordingly achieving the fluorescence switching for amplified sensing of low-abundance molecules. It is worth noting that nucleases and complex secondary structures are not involved in the entire system, offering a simple and flexible design. Furthermore, the novel and red-emissive DNA Ag NCs are employed as signal reporting, avoiding expensive and time-consuming organic fluorophore labeling. Experiment results demonstrate that this newly developed biosensing platform has a high signal-to-noise (∼15-folds), low limit of detection (1.59 pM), and good specificity to H5N1 DNA. Importantly, it can be used for H5N1 DNA detection in complex biological samples with a satisfactory recovery.

Fluorescence Sensors for the Detection of L-Histidine Based on Silver Nanoclusters Modulated by Copper Ions.

In this study, Cu2+ modulated silver nanoclusters were constructed for the turn-on, label-free detection of L-histidine. Six Ag NCs protected by oligonucleotides (DNA-Ag NCs) were tested in a series of experiments. Finally, A-DAN-Ag NCs were chosen as the best candidate due to their excellent fluorescent properties. The fluorescence of A-DAN-Ag NCs was quenched using Cu2+ through energy or electron transfer. However, quenched fluorescence could be restored dramatically in the presence of L-histidine due to Cu2+ liberation from A-DAN-Ag NCs and because of the chelation between the imidazole group of L-histidine and Cu2+. The proposed sensor exhibited high selectivity towards L-histidine over other amino acids, with a limit of detection (LOD) of 0.096 μM ranging from 0 to 8 μM. The proposed sensor succeeded in detecting L-histidine in diluted human urine. Therefore, the sensor has promising practical applications in biological systems.

Validating the reconstruction of DNA silver nanoclusters induced by different DNA sequence via HPLC and exploring the optical properties of reconstructed DNA silver nanoclusters

We investigated the influence of redundant DNA templates on the optical properties of DNA-stabilized silver nanoclusters (DNA AgNCs).

Highly Sensitive Fluorescence Detection of Three Organophosphorus Pesticides Based on Highly Bright DNA-Templated Silver Nanoclusters

It is still challenging to achieve simultaneous and sensitive detection of multiple organophosphorus pesticides (OPs). Herein, we optimized the ssDNA templates for the synthesis of silver nanoclusters (Ag NCs). For the first time, we found that the fluorescence intensity of T base-extended DNA-templated Ag NCs was over three times higher than the original C-riched DNA-templated Ag NCs. Moreover, a "turn-off" fluorescence sensor based on the brightest DNA-Ag NCs was constructed for the sensitive detection of dimethoate, ethion and phorate. Under strong alkaline conditions, the P-S bonds in three pesticides were broken, and the corresponding hydrolysates were obtained. The sulfhydryl groups in the hydrolyzed products formed Ag-S bonds with the silver atoms on the surface of Ag NCs, which resulted in the aggregation of Ag NCs, following the fluorescence quenching. The fluorescence sensor showed that the linear ranges were 0.1-4 ng/mL for dimethoate with a limit of detection (LOD) of 0.05 ng/mL, 0.3-2 µg/mL for ethion with a LOD of 30 ng/mL, and 0.03-0.25 µg/mL for phorate with a LOD of 3 ng/mL. Moreover, the developed method was successfully applied to the detection of dimethoate, ethion and phorate in lake water samples, indicating a potential application in OP detection.

Sensitive Fluorescent Determination of Nucleic Acids by a Cytosine-Rich Loop and Silver Nanoclusters in the Hybridization Chain Reaction (HCR)

Deep understanding of the effect of DNA sequence and structure on the fluorescent properties of DNA-templated silver nanoclusters (DNA–Ag NCs) affords alternative strategies for developing and exploiting DNA biosensors. DNA secondary structures (e.g., DNA loop) are essential for generating highly emissive DNA–Ag NCs. In this study, a cytosine-rich DNA loop was used as a facile template for the formation of silver nanoclusters. The fluorescence of silver nanocluster encapsulated within a cytosine-rich DNA loop was turned on by switching the size of the loop from large to small. Target nucleic acid served as the trigger for the hybridization chain reaction of hairpin probe 1 (H1) containing an inactivated cytosine-rich DNA loop with a large size at the ends and hairpin probe 2 (H2). Long-nicked double helices were obtained coupled with the opening of the large-size cytosine-rich DNA loop in H1 and switching to an activated cytosine-rich DNA loop with a small size. As a result, an increase in the fluorescent signal was observed. A sensitive detection limit of 10 pM and a linear detection range from 10 pM to 400 nM were obtained for nucleic acid determination. This facile assay provides a new approach capable of switching the fluorescence emission of DNA–Ag NCs for nucleic acid biosensing.

Label-Free Fluorescent Turn-On Glyphosate Sensing Based on DNA-Templated Silver Nanoclusters.

In this work, a label-free fluorescent detection method for glyphosate, based on DNA-templated silver nanoclusters (DNA-Ag NCs) and a Cu2+-ion-modulated strategy, was developed. In the presence of Cu2+, the fluorescence of the DNA-Ag NCs was quenched. Glyphosate can restore the fluorescence of DNA-Ag NCs. By analyzing the storage stability of the obtained DNA-Ag NCs using different DNA templates, specific DNA-Ag NCs were selected for the construction of the glyphosate sensor. The ultrasensitive detection of glyphosate was achieved by optimizing the buffer pH and Cu2+ concentration. The sensing of glyphosate demonstrated a linear response in the range of 1.0–50 ng/mL. The limit of detection (LOD) was 0.2 ng/mL. The proposed method was successfully applied in the detection of glyphosate in a real sample, indicating its high application potential for glyphosate detection.

DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review

Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.

A label-free aptasensor for the detection of ATP based on turn-on fluorescence DNA-templated silver nanoclusters

A label-free aptasensor has been fabricated in order to detect adenosine triphosphate (ATP) using turn-on fluorescence DNA-Ag NCs. The fluorescence of the DNA-Ag NCs could increase remarkably with the addition of ATP mainly because ATP specifically interacts with its aptamer to change the microenvironment of the darkish DNA-Ag NCs located at one terminus or two termini due to the conformational alteration of the aptamer structure. The proposed sensor can detect ATP in a linear range of 6-27 mM with a good detection limit of 5.0 μM. Additionally, the proposed method succeeded in detecting ATP in fetal bovine serum.

Rational Engineering of the DNA Walker Amplification Strategy by Using a Au@Ti3C2@PEI-Ru(dcbpy)32+ Nanocomposite Biosensor for Detection of the SARS-CoV-2 RdRp Gene.

The detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for preventing and controlling infectious diseases and disease treatment. In this work, a Au@Ti3C2@PEI-Ru(dcbpy)32+ nanocomposite-based electrochemiluminescence (ECL) biosensor was rationally designed, which realized sensitive detection of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2. In addition, a DNA walker was also used to excise the hairpin DNAs under the action of Nb.BbvCI endonuclease. Furthermore, model DNA–Ag nanoclusters (model DNA–AgNCs) were used to quench the initial ECL signal. As a result, the ECL biosensor was used to sensitively detect the SARS-CoV-2 RdRp gene with a detection range of 1 fM to 100 pM and a limit of detection of 0.21 fM. It was indicated that the ECL biosensor had a great application potential for clinical medical detection. Furthermore, the DNA walker amplification also played a reliable candidate strategy for other detection methods.

The effect of deuterium on the photophysical properties of DNA-stabilized silver nanoclusters.

We investigated the effect of using D2O versus H2O as solvent on the spectroscopic properties of two NIR emissive DNA-stabilized silver nanoclusters (DNA–AgNCs). The two DNA–AgNCs were chosen because they emit in the same energy range as the third overtone of the O–H stretch. Opposite effects on the ns-lived decay were observed for the two DNA–AgNCs. Surprisingly, for one DNA–AgNC, D2O shortened the ns decay time and enhanced the amount of µs-lived emission. We hypothesize that the observed effects originate from the differences in the hydrogen bonding strength and vibrational frequencies in the two diverse solvents. For the other DNA–AgNC, D2O lengthened the ns decay time and made the fluorescence quantum yield approach unity at 5 °C.

Correction to "Aptamer-Based Fluorescent Biosensing of Adenosine Triphosphate and Cytochrome c via Aggregation-Induced Emission Enhancement on Novel Label-Free DNA-Capped Silver Nanoclusters/Graphene Oxide Nanohybrids".

Four fluorescent DNA-stabilized fluorescent silver nanoclusters (DNA–AgNCs) were designed and synthesized with differences in lengths of cytosine-rich DNA strand (as the stabilizing agent) and targ...

A DNA rolling motor for photoelectrochemical biosensing of oral cancer overexpressed 1

Herein, a photoelectrochemical (PEC) biosensor has been constructed depending on DNA rolling motor and the synergistic effect among graphene oxide (GO), hemin and DNA-templated silver nanoclusters (DNA-Ag NCs) for oral cancer overexpressed 1 (ORAOV1) detection. Target-triggered catalytic hairpin assembly (CHA) cycling strategy has been adopted for signal amplification. Because of the excellent photoelectric behaviors, the compounds of graphene oxide and hemin (GO/hemin) have been used as photoelectric material. DNA-Ag NCs have been employed as signal amplification labels to enhance PEC responses. Scanning electron microscopy (SEM) was used to record the morphologies of nanomaterials. PEC and electrochemical analytical methods were employed to investigate the stepwise modification of the constructed biosensor. As a result, the proposed sensing platform has exhibited excellent analytical performance to ORAOV1 in a linear range from 1.0 × 10−15 to 1.0 × 10-10 mol·L-1 with the detection limit of 3.3 × 10-16 mol·L-1. It can achieve sensitive detection of ORAOV1 in saliva samples. The sensing system not only shows good selectivity and remarkable stability, but also provides a new method for the prevention, early assessment and post-treatment of diseases.

An ultrasensitive electrochemiluminescence resonance energy transfer biosensor for divalent mercury monitoring

An electrochemiluminescence (ECL) sensing approach was designed for sensitive Hg2+ detection based on oligonucleotide hosted silver cluster (DNA-Ag NCs) as effective unit for switching the ECL signal of graphite-like carbon nitride nanosheets (g-C3N4 NSs). In this system, g-C3N4 NSs were first immobilized on the glassy carbon electrode surface followed by the chitosan coating and probe DNA assembly. The g-C3N4 NSs exhibited stable ECL intensity which was regarded as first signal switch “on” state. DNA-Ag NCs can be captured onto the g-C3N4 NSs coated electrode surface via DNA hybridization, leading to the ECL signal quenching of g-C3N4 NSs attributed to the ECL resonance energy transfer (ECL-RET) between the luminophore donor g-C3N4 NSs and the acceptor DNA-Ag NCs, turning to signal “off” state. While in the presence of Hg2+, the formation of T-Hg2+-T coordination between DNA-Ag NCs or DNA-Ag NCs themselves would hinder DNA-Ag NCs from embellishing on the electrode surface, resulting in the recovery of the g-C3N4 NSs ECL intensity corresponding to the last signal switch “on” state. Based on this, the biosensor can be demonstrated to quantitatively analyze Hg2+ with a detection of limit of 5 pM. The proposed ECL platform has been utilized to sensitive and selective monitoring Hg2+ in environmental water samples.

Catalytic hairpin assembly induced dual signal enhancement for rapid detection of miRNA using fluorescence light-up silver nanocluster

A novel method of catalytic hairpin assembly (CHA) induced dual signal enhancement is developed for rapid detection of miRNA based on fluorescence light-up silver nanocluster (Ag NC). By the hybridization of a hairpin DNA and a single-stranded DNA, a unique probe is firstly designed. In the terminals of this probe, DNA-Ag NCs can be formed and display very weak fluorescence. In the presence of the target miRNA, the reaction of CHA can be triggered, forming two kinds of double-stranded complexes, in which the terminal DNA-Ag NCs are in close proximity to G-rich overhangs and the fluorescent signal can be dramatically enhanced. Compared with many other enzyme-based amplification strategies, this one exhibits distinct advantages of simplicity in experimental operation and a rapid detection process (within 1 h). Moreover, this assay exhibits an excellent selectivity and is successfully applied in the detection of miRNAs in complex biological media, which confirms the reliability and practicality of this protocol.

Rapid detection and cellular fluorescence imaging of the TBI biomarker Let-7i using a DNA–AgNC nanoprobe

Rapid fluorescence detection of Let-7i for TBI diagnosis and intracellular imaging have been studied using the multifunctional DNA–AgNCs.

Preparation and characterization of solid DNA silver nanoclusters with superior aerobic and thermal stability.

In the current study, we present a universal method to preserve DNA-templated silver nanoclusters (DNA AgNCs) in the solid-state. Our results show that DNA AgNCs must be precipitated before drying. By drying the ethanol precipitated DNA AgNCs, we have successfully prepared solid DNA AgNCs with superior stability in aerobic and high-temperature environments. Although the fluorescence lifetime measurements show that the emission of DNA AgNCs is drastically quenched in the solid-state, the emission can be fully recovered in solution. To our knowledge, this is the first attempt to prepare DNA AgNCs in solid-state, and this finding provides an ideal solution for the transportation and long-term preservation of DNA AgNCs.

Cationic-Polyelectrolyte-Modified Fluorescent DNA-Silver Nanoclusters with Enhanced Emission and Higher Stability for Rapid Bioimaging.

DNA-templated silver nanoclusters (DNA-Ag NCs) have shown great potential in various bioanalysis and bioimaging applications, owing to their facile synthesis and ultrasmall sizes and especially their programmable fluorescence emission depending on the sequences of DNA templates. However, the bioimaging applications of DNA-Ag NCs are severely limited by their poor stability in physiological environments and their poor cell permeability, resulting from the highly negatively charged DNA backbones. In this paper, cationic polyelectrolytes were used to modify fluorescent DNA-Ag NCs via electrostatic interactions between the positive polymer backbones and the negatively charged phosphate groups of the DNA strands. The fluorescence properties of a typical single-stranded-DNA (ssDNA)-templated Ag NC changed dramatically after incorporation with the cationic polyelectrolyte caused by conformational changes in the DNA, with a 3-fold fluorescence-emission enhancement of the Ag NCs observed after incorporation with a typical cationic polyelectrolyte, poly(diallyldimethylammonium chloride) (PDDA), whereas the fluorescence of double-stranded-DNA (dsDNA)-templated Ag NCs changed little after incorporation. Moreover, the modification with PDDA greatly prolonged the stability of both ssDNA- and dsDNA-stabilized Ag NCs against nuclease digestion and enhanced the cell uptake of the DNA-Ag NCs.Rapidcell imaging was demonstrated using NIH/3T3 cells as a model system.

A Turn-On Detection of DNA Sequences by Means of Fluorescence of DNA-Templated Silver Nanoclusters via Unique Interactions of a Hydrated Ionic Liquid.

Nucleic acid stability and structure, which are crucial to the properties of fluorescent DNA-templated silver nanoclusters (DNA-Ag NCs), significantly change in ionic liquids. In this work, our purpose was to study DNA-Ag NCs in a buffer containing the hydrated ionic liquid of choline dihydrogen phosphate (choline dhp) to improve fluorescence for application in DNA detection. Due to the stabilisation of an i-motif structure by the choline cation, a unique fluorescence emission—that was not seen in an aqueous buffer—was observed in choline dhp and remained stable for more than 30 days. A DNA-Ag NCs probe was designed to have greater fluorescence intensity in choline dhp in the presence of a target DNA. A turn-on sensing platform in choline dhp was built for the detection of the BRCA1 gene, which is related to familial breast and ovarian cancers. This platform showed better sensitivity and selectivity in distinguishing a target sequence from a mutant sequence in choline dhp than in the aqueous buffer. Our study provides new evidence regarding the effects of structure on properties of fluorescent DNA-Ag NCs and expands the applications of fluorescent DNA-Ag NCs in an ionic liquid because of improved sensitivity and selectivity.

How G-quadruplex topology and loop sequences affect optical properties of DNA-templated silver nanoclusters

In the study of the fabrication of DNA-templated silver nanoclusters (DNA-Ag NCs), how templates affect the fluorescence of the nanoclusters remains unclear, and it has been a challenge to understand the correlation between the properties of the DNA template and the Ag NCs. In this respect, based on the rational design of a series of structurally defined intramolecular G-quadruplexes, we prepared G-quadruplex-templated Ag NCs with a defined G-tetrad-to-silver ratio of 1:2. We evaluated the effect of G-quadruplex topology and loop sequences on the fluorescence of DNA-Ag NCs using circular dichroism, and extinction and emission spectroscopy. G-quadruplex templates with an anti-parallel topology were found to produce Ag NCs with stronger fluorescence compared with parallel and hybrid configurations. Loop bases adjacent to G-tetrads have a more significant impact on the fluorescence of Ag NCs compared with those in the middle of the loop, with adenine largely exhibiting an enhancement effect and thymine being detrimental. Generally, G-quadruplexes having an anti-parallel topology with adenine in the loop adjacent to the G-tetrad would be good templates for producing highly fluorescent Ag NCs. This is the first study to focus on the correlation between G-quadruplex topology/sequence and the optical properties of Ag NCs. We hope that the results of this study will facilitate a more in-depth understanding of correlation between G-quadruplex templates and Ag NCs, and help to understand and utilize their unique attributes.