DNA-regulated silver nanoclusters for label-free ratiometric fluorescence detection of DNA

Nanozyme's catalytic activity at neutral pH: reaction substrates and application in sensing

Nanozymes exhibit their great potential as alternatives to natural enzymes. In addition to catalytic activity, nanozymes also need to have biologically relevant catalytic reactions at physiological pH to fit in the definition of an enzyme and to achieve efficient analytical applications. Previous reviews in the nanozyme field mainly focused on the catalytic mechanisms, activity regulation, and types of catalytic reactions. In this paper, we discuss efforts made on the substrate-dependent catalytic activity of nanozymes at neutral pH. First, the discrepant catalytic activities for different substrates are compared, where the key differences are the characteristics of substrates and the adsorption of substrates by nanozymes at different pH. We then reviewed efforts to enhance reaction activity for model chromogenic substrates and strategies to engineer nanomaterials to accelerate reaction rates for other substrates at physiological pH. Finally, we also discussed methods to achieve efficient sensing applications at neutral pH using nanozymes. We believe that the nanozyme is catching up with enzymes rapidly in terms of reaction rates and reaction conditions. Designing nanozymes with specific catalysis for efficient sensing remains a challenge.

Ratiometric Electrochemical Biosensing of Methyltransferase Activity

In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).

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.

Ratiometric fluorescent sensor based on 2D MOF nanosheets modified by DNA for sensitive detection of Hg2

Mercury is highly toxic and can accumulate throughout the food cycle, leading to water contamination and foodstuffs pollution. Therefore, increasing attention has been paid to explore effective detection of Hg²⁺. Here, we report a sensitive Hg²⁺sensor based on single-stranded DNA (ssDNA) modified two-dimensional (2D) MOF nanosheets by a ratiometric fluorescent method. The chosen 2D MOF nanosheets possess intrinsic peroxidase-like catalytic ability, ssDNA adsorption and fluorescence quenching. We demonstrate that the adsorption of ssDNA can significantly improve the peroxidase mimetic activity of 2D MOF nanosheets, enhancing the fluorescence of substrate Amplex Red. Taking advantages of the favorable characteristics above, we fabricate an efficient Hg²⁺sensor. In the presence of Hg²⁺, the ssDNA is released from 2D MOF nanosheets, which results in a decreasing of peroxidase mimetic activity of 2D MOF nanosheets and a fluorescence enhancement of attached fluorophore. A linear relationship between ratiometric fluorescence of substrate and fluorophore and Hg²⁺concentrations is obtained. The detection limit is 5 nM, which is much lower than the maximal contamination level in drinking water (30 nM) by Word Health Organization. These findings show 2D MOF based ratiometric fluorescent sensor is a convenient and efficient strategy to detect Hg²⁺.

Nanomaterial-Based Dual-Emission Ratiometric Fluorescent Sensors for Biosensing and Cell Imaging

Owing to the unique optophysical properties of nanomaterials and their self-calibration characteristics, nanomaterial-based (e.g., polymer dots (Pdots) quantum dots (QDs), silicon nanorods (SiNRs), and gold nanoparticle (AuNPs), etc.) ratiometric fluorescent sensors play an essential role in numerous biosensing and cell imaging applications. The dual-emission ratiometric fluorescence technique has the function of effective internal referencing, thereby avoiding the influence of various analyte-independent confounding factors. The sensitivity and precision of the detection can therefore be greatly improved. In this review, the recent progress in nanomaterial-based dual-emission ratiometric fluorescent biosensors is systematically summarized. First, we introduce two general design approaches for dual-emission ratiometric fluorescent sensors, involving ratiometric fluorescence with changes of one response signal and two reversible signals. Then, some recent typical examples of nanomaterial-based dual-emission ratiometric fluorescent biosensors are illustrated in detail. Finally, probable challenges and future outlooks for dual-emission ratiometric fluorescent nanosensors for biosensing and cell imaging are rationally discussed.

Noble Metal Nanomaterial-Based Biosensors for Electrochemical and Optical Detection of Viruses Causing Respiratory Illnesses

Noble metal nanomaterials, such as gold, silver, and platinum, have been studied extensively in broad scientific fields because of their unique properties, including superior conductivity, plasmonic property, and biocompatibility. Due to their unique properties, researchers have used them to fabricate biosensors. Recently, biosensors for detecting respiratory illness-inducing viruses have gained attention after the global outbreak of coronavirus disease (COVID-19). In this mini-review, we discuss noble metal nanomaterials and associated biosensors for detecting respiratory illness-causing viruses, including SARS-CoV-2, using electrochemical and optical detection techniques. this review will provide interdisciplinary knowledge about the application of noble metal nanomaterials to the biomedical field.

Ratiometric Fluorescence Detection of DNA Based on the Inner Filter Effect of Ru(bpy)2(dppx)2+ toward Silicon Nanodots

A ratiometric DNA sensor was developed based on fluorescent silicon nanodots (SiNDs) and Ru(bpy)₂(dppx)²⁺. The absorption spectrum of Ru(bpy)₂(dppx)²⁺ has significant overlap with both the excitation and emission spectra of SiNDs. Therefore, fluorescence quenching of Ru(bpy)₂(dppx)²⁺ toward SiNDs can occur on account of the strong inner filter effect. The effect of quenching is not influenced by the specific binding between Ru(bpy)₂(dppx)²⁺ and DNA. Fluorescence turn-on detection of DNA can be performed employing Ru(bpy)₂(dppx)²⁺ and SiNDs as the response and reference signals, respectively. Using SiND-Ru(bpy)₂(dppx)²⁺, a convenient, sensitive, rapid, and precise method could be developed for DNA detection. In aqueous solutions, the I ₆₀₁/I ₄₄₈ fluorescence intensity ratio of SiND-Ru(bpy)₂(dppx)²⁺ increases linearly in the DNA concentration range of 20-1500 nM. The limit of detection and precision of the method is 4.3 nM and 3.5% (50 nM, n = 13), respectively. The ratiometric sensor was tested for visual detection of trace DNA. Moreover, this method was found suitable for the ratiometric detection of DNA in a simulated sample and a human serum sample, and the recoveries were in the range of 98-119%.

o-Phenylenediamine/gold nanocluster-based nanoplatform for ratiometric fluorescence detection of alkaline phosphatase activity

This study demonstrates a novel and convenient ratiometric fluorescent method for the detection of alkaline phosphatase (ALP) activity. Amino-functionalized mesoporous silica nanoparticle-gold nanoclusters (MSN-AuNCs) nanocomposites were integrated with o-phenylenediamine (OPD) to form a ratiometric fluorescence nanoplatform. The presence of ALP induced the generation of quinoxaline (QX) derivative which called 3-(dihydroxyethyl)furo[3,4-b]quinoxaline-1-one (DFQ) with strong fluorescence emission at 450 nm, while the orange-red fluorescence of MSN-AuNCs at 580 nm was slightly quenched. Meanwhile, an obvious fluorescence color change from orange-red to purple and finally to blue can be observed by naked eyes with the increasing of ALP concentration. Therefore, employing the fluorescence emission of DFQ at 450 nm as the reporter signal and the fluorescence emission of MSN-AuNCs at 580 nm as a reference signal, a sensitive ratiometric detection method for ALP was developed. Quantitative detection of ALP activity in the linear range from 0.2 to 80 U/L with a detection limit of 0.1 U/L can be realized in this way, which endows the assay with high sensitivity enough for practical detection of ALP in human serum samples.

DNA bioassays based on the fluorescence 'turn off' of silver nanocluster beacon

Recognition and quantification of oligonucleotide sequences play important roles in medical diagnosis. In this study, a new fluorescent oligonucleotide-stabilized silver nanocluster beacon (NCB) probe was designed for sensitive detection of oligonucleotide sequence targets. This probe contained two tailored DNA strands. One strand was a signal probe strand containing a cytosine-rich strand template for fluorescent silver nanocluster (Ag NC) synthesis and a detection sections at each end. The other strand was a fluorescence enhancing strand containing a guanine-rich section for signal enhancement at one end and a linker section complementary to one end of the signal probe strand. After synthesis of the Ag NCs and hybridization of the two strands, the fluorescence intensity of the as-prepared silver NCB was enhanced 200-fold compared with the Ag NCs. Two NCBs were designed to detect two disease-related oligonucleotide sequences, and results indicated that the two target oligonucleotide sequences in the range 50.0-600.0 and 50.0-200.0 nM could be linearly detected with detection limits of 20 and 25 nM, respectively. The developed fluorescence method using NCBs for oligonucleotide sequence detection was sensitive, facile and had potential for use in bioanalysis and diagnosis.

A Ratiometric Fluorescent DNA Radar Based on Contrary Response of DNA/Silver Nanoclusters and G-Quadruplex/Crystal Violet

G-quadruplex (G4) exhibits infinite application foreground due to its special properties and critical roles in biological regulation. A DNA radar was first built by assigning the silver nanocluster (AgNC) as the radar transmitter, the middle single strand DNA-bridge connected on the AgNCs as the electromagnetic wave, and the G4/crystal violet complex as the radar antenna. The radar antenna could receive the signal of the target DNA that met the electromagnetic wave and give a location via light-up fluorescence. Here, G4 is chosen as the suitable template to connect potential nanomaterial AgNCs with the G4 binder (crystal violet, CV) since the rich guanine in G4 could not only enhance the fluorescence of AgNCs but also form quartets offering powerful binding sites for the G4 binder. Meanwhile, the hybridization behavior of the middle single strand-bridge produced contrary effects decreasing the fluorescence of AgNCs and increasing the fluorescence of G4/CV, which vests a ratiometric feature in such DNA radar. Additionally, this DNA radar model could realize a cascade of logic circuits, the construction of a 1-to-2 decoder, and the ratiometric detection of target DNA. This system could also be employed for DNA detection in a biological matrix, which could be potentially usable as a unique means for monitoring the pathological process of disease, and lays the foundation for the future treatment of diseases.

Ratiometric fluorescence monitoring of α-glucosidase activity based on oxidase-like property of MnO2 nanosheet and its application for inhibitor screening

In recent years, α-glucosidase (α-Glu) inhibitor has been widely used in clinic for diabetic and HIV therapy. Although different systems have been constructed for sensitive and selective detection of α-Glu and screening its inhibitor, the method based on ratiometric fluorescence for α-glucosidase inhibitor screening remains poorly investigated. Herein, we constructed a new MnO₂ nanosheet (NS)-based ratiometric fluorescent sensor for α-glucosidase activity assay and its inhibitor screening. MnO₂ NS as an oxidase-mimicking nanomaterial directly oxidized o-phenylenediamine (OPD) into 2,3-diaminophenazine (DAP) which had a strong fluorescence emission at 575 nm, whereas the fluorescence of Ag nanoclusters (NCs) at 450 nm was then quenched by the generated DAP through inner filter effect (IFE). When 2-O-α-d-glucopyranosyl-l-ascorbic acid (AAG) as α-Glu substrate and α-Glu were introduced into the above system, MnO₂ NS would be reduced to Mn²⁺ and lose the oxidase-like property since ascorbic acids (AA) were released with the hydrolysis of AAG by α-Glu. Thus, DAP would not be produced and IFE was stopped accompanying with the fluorescence decrease of DAP and fluorescence increase of AgNCs. A ratiometric fluorescent α-Glu nanosensor was thus developed. The fluorescence intensity ratio of DAP to AgNCs linearly decreased with the increasing of α-Glu concentrations in the range of 0.2-8 U mL^-1, and limit of detection was 0.03 U mL^-1. This proposed sensing approach was also expanded to α-Glu inhibitor screening and showed excellent applicability. As a typical α-Glu inhibitor, acarbose was investigated with a low detection limit of 10^-8 M. The constructed sensor platform was proven to be sensitive and selective as well as simple, label-free and low-cost, making it promising for the accurate diagnosis of relevant disease and discovery of potential drugs.

Melamine-promoted formation of bright and stable DNA-silver nanoclusters and their antimicrobial properties

A new method has been developed for the preparation of brightly fluorescent and stable DNA-silver nanoclusters (DNA-AgNCs). The approach takes advantage of specific interactions occurring between melamine and thymine residues in a DNA template. These interactions cause the formation of a melamine-DNA-AgNC complex (Mel-DNA-AgNCs), in which a change in the environment of the DNA template causes binding of additional Ag⁺ and an enhancement in the fluorescence efficiency and stability. The effects of the nature of the template DNA, DNA : Ag⁺ : NaBH₄ ratio, pH and temperature were systematically assessed in order to maximize the melamine-promoted fluorescence enhancement. The results show that the Mel-DNA-AgNCs, generated under the optimal conditions, exhibit a ca. 3-fold larger fluorescence efficiency and long-term stability (70 d) in contrast to those of DNA-AgNCs in the absence of melamine. Importantly, the bright and stable Mel-DNA-AgNCs exhibit antimicrobial activities against Gram-positive and Gram-negative bacteria that are superior to those of DNA-AgNCs alone. To the best of our knowledge, this is the first report describing the synthesis of DNA-AgNCs that have improved fluorescence efficiencies and that function as effective antimicrobial agents.

A duplex connection can further illuminate G-quadruplex/crystal violet complex

Duplex-connected G-quadruplex (dsG4) has a more evident promotion of the fluorescent emission of crystal violet than pure G-quadruplex (G4), which is firstly found and investigated systematically using fluorescence spectra, circular dichroism, and density functional theory. This new phenomenon also shows potential in application for target nucleic acid detection.

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.

The solid DNA AgNCs exhibit superior stability and the fluorescence can be recovered in solution.

An ATP-fueled nucleic acid signal amplification strategy for highly sensitive microRNA detection

Herein, an adenosine triphosphate (ATP)-fueled nucleic acid signal amplification strategy based on toehold-mediated strand displacement (TMSD) and fluorescence resonance energy transfer (FRET) was proposed for highly sensitive detection of microRNA-21. More importantly, the target microRNA-21 could be regenerated with ATP as the fuel rather than a nucleotide segment in conventional approaches, which made the proposed strategy simple and efficient due to the high affinity and strength of the aptamer-target interaction.

Logic circuit controlled multi-responsive branched DNA scaffolds

A logic circuit controlled multi-responsive sensing platform built on a three-way DNA junction (TWJ) is reported. It enabled the construction of novel fluorescent sensing platforms responsive to any target out of HIV gene, ATP and pH value, and furthermore were logically regulated by two other targets and then behaved as different logic circuits, which consist of two tandem AND gates or cascaded NAND and INH gates by varying the positions of the fluorescent tags.

Ultrasensitive aptamer biosensor for arsenic (III) detection based on label-free triple-helix molecular switch and fluorescence sensing platform

Arsenic ion is a well-known harmful heavy element widely existing in the environment. Arsenic pollution occurring frequently has become increasing a serious worldwide threat to human health and the environment. The development of sensitive and reliable methods to detect As³⁺ in water is of great importance to biochemical research and monitoring applications. Herein, a label-free fluorescence sensing platform was elaborately designed for As³⁺ monitoring using exonuclease III (Exo III)-assisted cascade target recycling amplification strategy. The triple-helix molecular switch was employed as the sensing element and 2-amino-5,6,7-trimethyl-1,8-naphthyridine was used as the signal indicator. The resulting biosensor is simple, ultrasensitive, and exhibits a limit of detection of 5 ng/L with high selectivity. Meanwhile, the proposed sensor is successfully applied to determination of As³⁺ in practical sample analysis (tap water, lake water and pond water). The results shown herein have important implications in the development of new fluorescent sensors for the fast, easy, and selective detection and quantification of As³⁺ in water samples. More importantly, the proposed platform can be extended to detect other heavy metal ions with newly designed triple-helix molecular switch, as well as pesticide residue, antibiotic residues, and biomarkers by using aptamer sequences.

In situ fluorescence activation of DNA-silver nanoclusters as a label-free and general strategy for cell nucleus imaging

A facile, general and turn-on nucleus imaging strategy was first developed based on in situ fluorescence activation of C-rich dark silver nanoclusters by G-rich telomeres. After a simple incubation without washing, nanoclusters could selectively stain the nucleus with intense red luminescence, which was confirmed using fixed/living cells and several cell lines.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

A reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue to DNA with alternating AT base sequence for sensitive detection of adenosine

We develop a reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue (MB) to DNA with alternating AT base sequence for sensitive detection of adenosine. We design a strand 1 with MB-modified thymine (T) base in the proximal 3' termini as the capture probe for its immobilization on the gold electrode and a 3' termini ferrocene (Fc)-modified aptamer for the recognition of adenosine. The hybridization of strand 1 with the aptamer leads to the formation of a double-stranded DNA (dsDNA) and consequently the away of MB from the electrode surface and the close of Fc to the electrode surface, generating a small value of I_MB/I_Fc (I_MB and I_Fc are the peak currents of MB and Fc, respectively). In the presence of adenosine, its binding with the aptamer induces the release of Fc from the electrode surface and the close of MB to the electrode surface, generating a large value of I_MB/I_Fc. As a result, adenosine may be accurately quantified by the measurement of ratiometric signal (I_MB/I_Fc). This ratiometric electrochemical biosensor can be simply fabricated and exhibits high sensitivity with a limit of detection of as low as 90.8pM and a large dynamic range from 0.1nM to 100μM. Moreover, this biosensor demonstrates good performance with excellent selectivity, regeneration capability, high reliability and good reproducibility, and may become a universal platform for the detection of various biomolecules which can be recognized by aptamers, holding great potential for further applications in biomedical research and clinical diagnosis.

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.

Introducing Ratiometric Fluorescence to MnO2 Nanosheet-Based Biosensing: A Simple, Label-Free Ratiometric Fluorescent Sensor Programmed by Cascade Logic Circuit for Ultrasensitive GSH Detection

Glutathione (GSH) plays crucial roles in various biological functions, the level alterations of which have been linked to varieties of diseases. Herein, we for the first time expanded the application of oxidase-like property of MnO₂ nanosheet (MnO₂ NS) to fluorescent substrates of peroxidase. Different from previously reported fluorescent quenching phenomena, we found that MnO₂ NS could not only largely quench the fluorescence of highly fluorescent Scopoletin (SC) but also surprisingly enhance that of nonfluorescent Amplex Red (AR) via oxidation reaction. If MnO₂ NS is premixed with GSH, it will be reduced to Mn²⁺ and lose the oxidase-like property, accompanied by subsequent increase in SC's fluorescence and decrease in AR's. On the basis of the above mechanism, we construct the first MnO₂ NS-based ratiometric fluorescent sensor for ultrasensitive and selective detection of GSH. Notably, this ratiometric sensor is programmed by the cascade logic circuit (an INHIBIT gate cascade with a 1 to 2 decoder). And a linear relationship between ratiometric fluorescent intensities of the two substrates and logarithmic values of GSH's concentrations is obtained. The detection limit of GSH is as low as 6.7 nM, which is much lower than previous ratiometric fluorescent sensors, and the lowest MnO₂ NS-based fluorescent GSH sensor reported so far. Furthermore, this sensor is simple, label-free, and low-cost; it also presents excellent applicability in human serum samples.

Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer

In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.

Ratiometric NanoCluster Beacon: A Label-Free and Sensitive Fluorescent DNA Detection Platform

Although researches until now have emphasized the influence of an oligonucleotide sequence on the fluorescence of oligonucleotide-stabilized silver nanoclusters (AgNCs), this influence has been explored as a novel ratiometric fluorescent signal transduction in this work. This study builds on our original discovery of a template-transformation phenomenon, which demonstrated that the connection of a special DNA fragment (5'-CACCGCTTT-3') with a green-emitting AgNC nucleation sequence (GNuS, 5'-TGCCTTTTGGGGACGGATA-3') creates a red-emitting AgNC nucleation sequence (RNuS, 5'-CACCGCTTTTGCCTTTTGGGGACGGATA-3'). Attempts to expand this idea and construct elegant ratiometric NanoCluster Beacons (NCBs) for DNA sequence detection are not straightforward, and, thus, we carried out a series of investigations with the goal of understanding the mechanism of this template-transformation phenomenon. Experimental results showed that the six-nucleotide fragment (5'-CACCGC-3') at the 5'-end of RNuS acts as a template convertor and takes full responsibility for the template transformation from GNuS to RNuS. Moreover, we found that the appropriate proximity of the convertor to GNuS also plays a significant role in the template transformation. We then show that the insights gained here for the template-transformation mechanism allow us to construct ratiometric NCBs by simply appending the convertor and the GNuS onto a rationally designed stem-loop probe. This new type of NCB emits intense red fluorescence without the addition of a target DNA and emerges as a new, bright green emission only when hybridized to its target DNA. By measuring the distinct variation in the fluorescence intensity ratios of green and red emission, this ratiometric NCB was demonstrated to sensitively detect Hepatitis-A virus gene sequences, a proof-of-concept target in this work, with good selectivity.

Systematic comparison between toehold exchange and toehold displacement: exploration for highly specific and sensitive DNA detection

The detection of nucleic acid variations with high specificity and sensitivity is essential for the good practice of precision medicine.

A sensitive ratiometric electrochemical biosensor based on DNA four-way junction formation and enzyme-assisted recycling amplification

We develop a ratiometric electrochemical biosensor for DNA assay based on DNA four-way junction formation and enzyme-assisted recycling amplification.

A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters

DNA-stabilized silver nanoclusters (AgNCs), the fluorescence emission of which can rival that of typical organic fluorophores, have made possible a new class of label-free molecular beacons for the detection of single-stranded DNA. Like fluorophore-quencher molecular beacons (FQ-MBs) AgNC-based molecular beacons (AgNC-MBs) are based on a single-stranded DNA that undergoes a conformational change upon binding a target sequence. The new conformation exposes a stretch of single-stranded DNA capable of hosting a fluorescent AgNC upon reduction in the presence of Ag(+) ions. The utility of AgNC-MBs has been limited, however, because changing the target binding sequence unpredictably alters cluster fluorescence. Here we show that the original AgNC-MB design depends on bases in the target-binding (loop) domain to stabilize its AgNC. We then rationally alter the design to overcome this limitation. By separating and lengthening the AgNC-stabilizing domain, we create an AgNC-hairpin probe with consistent performance for arbitrary target sequence. This new design supports ratiometric fluorescence measurements of DNA target concentration, thereby providing a more sensitive, responsive and stable signal compared to turn-on AgNC probes. Using the new design, we demonstrate AgNC-MBs with nanomolar sensitivity and singe-nucleotide specificity, expanding the breadth of applicability of these cost-effective probes for biomolecular detection.

Metal nanoclusters: novel probes for diagnostic and therapeutic applications

Metal nanoclusters, composed of several to a few hundred metal atoms, have received worldwide attention due to their extraordinary physical and chemical characteristics. Recently, great efforts have been devoted to the exploration of the potential diagnostic and therapeutic applications of metal nanoclusters. Here we focus on the recent advances and new horizons in this area, and introduce the rising progress on the use of metal nanoclusters for biological analysis, biological imaging, therapeutic applications, DNA assembly and logic gate construction, enzyme mimic catalysis, as well as thermometers and pH meters. Furthermore, the future challenges in the construction of biofunctional metal nanoclusters for diagnostic and therapeutic applications are also discussed. We expect that the rapidly growing interest in metal nanocluster-based theranostic applications will certainly not only fuel the excitement and stimulate research in this highly active field, but also inspire broader concerns across various disciplines.

Formation of Silver Nanoclusters from a DNA Template Containing Ag(I)-Mediated Base Pairs

A series of DNA double helices containing different numbers of silver(I)-mediated base pairs involving the artificial nucleobases imidazole or 2-methylimidazole has been applied for the generation of DNA-templated silver nanoclusters. The original Ag(I)-containing nucleic acids as well as the resulting nanoclusters and nanoparticles have been characterized by means of UV/Vis spectroscopy, circular dichroism (CD) spectroscopy, fluorescence spectroscopy, and transmission electron microscopy (TEM). The results show for the first time that metal-mediated base pairs can be used for the templated growth of metal nanoclusters.

Coupling a DNA–ligand ensemble with Ag cluster formation for the label-free and ratiometric detection of intracellular biothiols

A smart nanoprobe was constructed by coupling a DNA–ligand ensemble with Ag cluster formation for the ratiometric detection of intracellular biothiols.

Cascade DNA logic device programmed ratiometric DNA analysis and logic devices based on a fluorescent dual-signal probe of a G-quadruplex DNAzyme

Two fluorescence sensitive substrates of G4 DNAzyme with inverse responses were simultaneously used to a cascade advanced DNA logic device based DNA analysis for the first time.

Poly thymine stabilized copper nanoclusters as a fluorescence probe for melamine sensing

In this work, poly-thymine stabilized copper nanoclusters have been used as a fluorescence probe for melamine sensing for the first time. Melamine can bind to thymine through hydrogen bond, which could dramatically enhance the fluorescence intensity of poly-thymine stabilized copper nanoclusters. The enhancement factors (I-I0)/I0 increase linearly with the lgCmelamine over the melamine concentration range of 0.1 µM to 6 µM. The detection limit of melamine is 95 nM, which is 200 times lower than the US Food and Drug Administration estimate melamine safety limit 20 µM. Melamine in milk was detected with good recovery, which suggested that this novel fluorescence probe has great potential in practical application.

Target catalyzed hairpin assembly for constructing a ratiometric electrochemical aptasensor

In this paper, we develop a novel dual-signaling amplified aptasensor for protein detection via target-catalyzed hairpin assembly. Thrombin was chosen as a model target. This aptasensor contains two DNA hairpins termed as H1 and H2. H1, which is modified at its 3' ends with a methylene blue (MB), consists of the aptamer sequence of human thrombin. Meanwhile, H2 which is modified at its 3' ends with a ferrocene (Fc), is partially complementary to H1. Upon the addition of target protein, it can facilitate the opening of the hairpin structure of H1 and thus accelerate the hybridization between H1 and H2, the target protein can be displaced from hairpin H1 by hairpin H2 through a process similar to DNA branch migration. The released target found another H1 to trigger the cycle, resulting in the multiplication of the Fc confined near the GE surface and MB away from the GE surface. When IFc/IMB is used as the response signal for quantitative determination of thrombin, the detection limit (41 fM) is much lower than that by using either MB or Fc alone. This new dual-signaling aptasensor is readily regenerated and shows good response toward the target. Furthermore, this amplified aptasensor shows high selectivity toward its target protein. The clever combination of the functional DNA hairpin and the novel device achieved a ratiometric electrochemical aptasensor, which could be used as a simple, sensitive high repeatability and selective platform for target protein detection.

Label-free nucleic acids detection based on DNA templated silver nanoclusters fluorescent probe

Based on DNA templated Ag NCs (DNA/Ag NCs) fluorescent probe, a label-free fluorescent method was developed for the detection of clinical significant DNA fragments from human immunodeficiency virus type 1 (HIV-1) DNA. Firstly, a hairpin probe, containing target DNA recognition sequence and guanine-rich sequence, was designed to hybridize with the target DNA and form a blunt 3'-terminus DNA duplex. Then, exonuclease III (Exo III) was employed to stepwise hydrolyze the mononucleotides from formed blunt 3'-terminus DNA duplex, releasing the target DNA and guanine-rich sequence. Finally, DNA/Ag NCs fluorescent probe was introduced to hybridize with the guanine-rich sequence, leading to an enhanced fluorescence signal for detection. The proposed method could detect as low as 2.9×10(-10) mol L(-1) HIV-1 DNA and exhibited excellent selectivity against mismatched target DNA. Furthermore, the method possessed perfect recoveries in cells lysate and human serum, showing potential to be used in biological samples.