DNA-Ag nanoclusters as fluorescence probe for turn-on aptamer sensor of small molecules

As promising substitutes for organic dyes and quantum dots, few-atom fluorescent silver nanoclusters (Ag NCs) have recently gained much attention in a wide range from cellular imaging to chemical/biological detection applications owing to their ultrasmall size (<2 nm), excellent photostability, good biocompatibility and water solubility. Herein, we design an aptamer, guanine-rich (G-rich) DNA and Ag NCs nanocomplex to investigate its ability for the detection of small molecules. The design contains two DNA strands which are both chimeric conjugates of the DNA aptamer sequence fragment and G-rich sequence fragment. Using cocaine as a model molecule, the two DNA strands are in free state if there is no cocaine present, and the formed Ag NCs through the reduction of Ag(+) by NaBH(4) show weak fluorescence emission. In the presence of cocaine, however, the two aptamer fragments bind cocaine, which in turn puts the two G-rich sequence fragments in proximity and the fluorescent intensity of DNA-Ag NCs enhances greatly. As a result, DNA-Ag NCs are demonstrated as a novel, cost-effective and turn-on fluorescent probe for the analysis of cocaine, with a detection limit of 0.1 μM. Besides, successful detection of adenosine triphosphate (ATP) with detection limit of 0.2 μM demonstrates its potential to be a general method.     

Selective fluorescence quenching of papain–Au nanoclusters by self‐polymerization of dopamine

In this paper, we synthesized a papain‐stabilized fluorescent Au nanocluster (NC) probe and studied its interaction with dopamine. As fluorescence of papain–Au NCs is quenched in the presence of dopamine under alkaline conditions, we were able to establish a simple, selective analytical method for dopamine determination. By studying the fluorescence lifetime and dynamic light scattering of the NCs before and after interaction with dopamine, we found that this fluorescence quenching mechanism was possibly due to dopamine self‐polymerization that produced polydopamine that cross‐linked papain–Au NCs. Based on this new phenomenon, we proposed a highly selective analytical method for dopamine detection. Other small organic molecules, such as amino acids, ascorbic acid and uric acid did not interfere with dopamine detection. Dopamine in the range 20–100 μM can be linearly detected by the fluorescence quenching ratio of gold nanoclusters. Dopamine detection could be visually realized by watching color changes of papain–Au NCs under UV light or daylight, as both fluorescence and absorption of the papain–Au NCs changed during dopamine polymerization.     

Silver‐doped graphite carbon nitride nanosheets as fluorescent probe for the detection of curcumin

Green fluorescent silver (Ag)‐doped graphite carbon nitride (Ag‐g‐C₃N₄) nanosheets have been fabricated by an ultrasonic exfoliating method. The fluorescence of the Ag‐g‐C₃N₄ nanosheets is quenched by curcumin. The fluorescence intensity decreases with the increase in the concentration of curcumin, indicating that the Ag‐g‐C₃N₄ nanosheets can function as a non‐toxic and facile fluorescence probe to detect curcumin. The fluorescence intensity of Ag‐g‐C₃N₄ nanosheets shows a linear relationship to curcumin in the concentration range 0.01–2.00 μM with a low detection limit of 38 nM. The fluorescence quenching process between curcumin and Ag‐g‐C₃N₄ nanosheets mainly is based on static quenching. The fluorescent probe has been successfully applied to analyse curcumin in human urine and serum samples with satisfactory results.     

One-pot synthesis of fluorescent oligonucleotide Ag nanoclusters for specific and sensitive detection of DNA

In this study, we prepared fluorescent, functional oligonucleotide-stabilized silver nanoclusters (FFDNA-Ag NCs) through one-pot synthesis and then employed them as probes for single nucleotide polymorphisms (SNPs). The FFDNA-Ag NCs were obtained through the NaBH(4)-mediated reduction of AgNO(3) in the presence of a DNA strand having the sequence 5'-C(12)-CCAGATACTCACCGG-3'. The specific DNA scaffold combines a fluorescent base motif (C(12)) and a specific sequence (CCAGATACTCACCGG) that recognizes a gene for fumarylacetoacetate hydrolase (FAH). The sensing mechanism of our new probe is based on the FFDNA-Ag NCs having different stabilities (fluorescence intensities) in solutions containing 150 mM NaCl in the absence and presence of perfect match DNA (DNA(pmt)). Under the optimal conditions (150 mM NaCl, 20 mM phosphate solution, pH 7.0), the fluorescence ratios of the FFDNA-Ag NC probes in the presence and absence of DNA(pmt), plotted against the concentration of DNA(pmt), was linear over the range 25-1000 nM (R(2)=0.98), with a limit of detection (S/N=3) of 14 nM. This cost-effective and simple FFDNA-Ag NC probe is sensitive and selective for SNPs of a gene for FAH.     

Detection of silver(I) ions based on the controlled self-assembly of a perylene fluorescence probe

In the current work, we report a label-free fluorescence turn-on approach for the sensitive and selective sensing of Ag(+). A cationic perylene derivative, compound A, was used as the fluorescence probe. Compound A monomer is strongly fluorescent, and the fluorescence can be efficiently quenched through self-aggregation (self-assembly). A cytosine (C)-rich oligonucleotide, oligo-C, was employed. In the absence of Ag(+), oligo-C induced strong compound A aggregation due to electrostatic interactions in aqueous media, and very weak fluorescence signal was detected. However, in the presence of Ag(+), the specific interactions between oligo-C and Ag(+) induced hairpin structure formation of oligo-C through C-Ag(+)-C bonding interactions. Oligo-C binding to compound A aggregates was weakened; therefore, compound A monomer could be released and detected. The intensity of the fluorescence signal was directly related to the amount of Ag(+) added to the assay solution. Our method is highly sensitive-a limit of detection of 5nM was obtained-and also very selective. Ag(+) detection in complex sample mixtures was also demonstrated.     

Label‐free DNA sensor based on fluorescent cationic polythiophene for the sensitive detection of hepatitis B virus oligonucleotides

Water‐soluble fluorescent conjugated polymers can be used as an optical platform in highly sensitive DNA sensors. Here we report a simple label‐free DNA sensor using poly(3‐alkoxy‐4‐methylthiophene) to recognize and detect different oligonucleotide targets related to the YMDD gene mutation of hepatitis B virus. The concentration of surfactant Triton X‐100, NaCl, the oligonucleotide capture probe and the oligonucleotide hybridization conditions have a great impact on fluorescence intensity. Under the optimum conditions, two types of oligonucleotide targets involving YMDD gene mutation of hepatitis B virus were successfully recognized. Moreover, there was a linear relationship between fluorescence intensity and the concentration of oligonucleotide target. The detection limit of the wild‐type hepatitis B virus target is 88 pmol L^?1. Copyright © 2009 John Wiley & Sons, Ltd.     

Selective detection of nitrofurantoin by histidine-capped silver nanoclusters with blue luminescence

In view of the significance of nitrofurantoin, there is an urgent need for efficient analytical methods for accurate detection of nitrofurantoin. Considering their superior fluorescence performance and rarity of reports regarding nitrofurantoin detection by fluorescent silver nanoclusters (Ag NCs), Ag NCs with good stability and uniform size were synthesized through a simple method by protection of histidine (His) and reduction of ascorbic acid (AA). Based on the quenching by nitrofurantoin, Ag NCs were applied successfully in the detection of nitrofurantoin with high sensitivity. In the range of 0.5–150 μM, a linear relationship was found between ln(F₀/F) and nitrofurantoin amounts. Static quenching and inner filter effect were proved to be the main quenching mechanisms. Significantly superior selectivity and satisfactory recovery results in bovine serum indicate that Ag NCs provide a better choice for nitrofurantoin detection.     

Dramatic increase in the signal and sensitivity of detection <Emphasis Type="Italic">via</Emphasis> self-assembly of branched DNA

In molecular testing using PCR, the target DNA is amplified via PCR and the sequence of interest is investigated via hybridization with short oligonucleotide capture probes that are either in a solution or immobilized on solid supports such as beads or glass slides. In this report, we report the discovery of assembly of DNA complex(es) between a capture probe and multiple strands of the PCR product. The DNA complex most likely has branched structure. The assembly of branched DNA was facilitated by the product of asymmetric PCR. The amount of branched DNA assembled was increased five fold when the asymmetric PCR product was denatured and hybridized with a capture probe all in the same PCR reaction mixture. The major branched DNA species appeared to contain three reverse strands (the strand complementary to the capture probe) and two forward strands. The DNA was sensitive to S1 nuclease suggesting that it had single-stranded gaps. Branched DNA also appeared to be assembled with the capture probes immobilized on the surface of solid support when the product of asymmetric PCR was hybridized. Assembly of the branched DNA was also increased when hybridization was performed in complete PCR reaction mixture suggesting the requirement of DNA synthesis. Integration of asymmetric PCR, heat denaturation and hybridization in the same PCR reaction mixture with the capture probes immobilized on the surface of solid support achieved dramatic increase in the signal and sensitivity of detection of DNA. Such a system should be advantageously applied for development of automated process for detection of DNA.     

Silver nanoclusters stabilized with denatured fish sperm DNA and the application on trace mercury ions detection

In this study, fluorescent silver nanoclusters (Ag NCs) were synthesized using denatured fish sperm DNA as the template. In contrast to other methods, this method did not use artificial DNA as the template. After their reaction with denatured fish sperm DNA, Ag⁺ ions were reduced by NaBH₄ to form Ag NCs. The Ag NCs showed a strong fluorescence emission at 650 nm when excited at 585 nm. The fluorescence intensity increased fourfold at pH 3.78, controlled with Britton–Robinson buffer solution. The fluorescence of the Ag NCs was quenched in the presence of trace mercury ions (Hg²⁺) in a weakly acidic medium and nitrogen atmosphere. The extent of the fluorescence quenching of Ag NCs strongly depends on the Hg²⁺ ion concentration over a linear range from 2.0 nmol L^?1 to 3.0 μmol L^?1. The detection limit (3σ/k) for Hg²⁺ was 0.7 nmol L^?1. Thus, a sensitive and rapid method was developed for the detection of Hg²⁺ ions.     

ECHO-LNA conjugates: hybridization-sensitive fluorescence and its application to fluorescent detection of various RNA strands

Hybridization-sensitive fluorescent DNA probes containing the nucleotide units of locked nucleic acid (LNA) have been developed. Exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes that incorporated LNA nucleotides achieved high thermostability of the hybrid with target RNA strands. The appropriately designed ECHO-LNA chimeric probes exhibited an effective on-off switching property of fluorescence depending on hybridization with RNA and facilitated fluorescent detection of the TAR RNA strand forming a hairpin structure and distinction of one base difference in PLAC4 RNA sequence.     

Label-free electrical detection of DNA hybridization for the example of influenza virus gene sequences

Microarrays based on DNA-DNA hybridization are potentially useful for detecting and subtyping viruses but require fluorescence labeling and imaging equipment. We investigated a label-free electrical detection system using electrochemical impedance spectroscopy that is able to detect hybridization of DNA target sequences derived from avian H5N1 influenza virus to gold surface-attached single-stranded DNA oligonucleotide probes. A 23-nt probe is able to detect a 120-nt base fragment of the influenza A hemagglutinin gene sequence. We describe a novel method of data analysis that is compatible with automatic measurement without operator input, contrary to curve fitting used in conventional electrochemical impedance spectroscopy (EIS) data analysis. A systematic investigation of the detection signal for various spacer molecules between the oligonucleotide probe and the gold surface revealed that the signal/background ratio improves as the length of the spacer increases, with a 12- to 18-atom spacer element being optimal. The optimal spacer molecule allows a detection limit between 30 and 100 fmol DNA with a macroscopic gold disc electrode of 1 mm radius. The dependence of the detection signal on the concentration of a 23-nt target follows a binding curve with an approximate 1:1 stoichiometry and a dissociation constant of KD=13+/-4 nM at 295 K.     

Single-stranded DNAzyme-based Pb2+ fluorescent sensor that can work well over a wide temperature range

DNAzymes have become an excellent choice for sensing applications. Based on DNAzymes, three generations of Pb(2+) fluorescent sensors have been reported. In these sensors, two oligonucleotide strands (substrate strand and enzyme strand) were used, which not only increased the complexity of the detection system, but also brought some difficulties for the use of the sensors at elevated temperatures. To overcome this problem, a single-stranded DNAzyme-based Pb(2+) fluorescent sensor was designed by combining the substrate sequence and the enzyme sequence into one oligonucleotide strand. The intramolecular duplex structure of this single-stranded DNAzyme kept the fluorophore and the quencher, labeled at its two ends, in close proximity; thus the background fluorescence was significantly suppressed. Using this fluorescent sensor, Pb(2+) quantitation can be achieved with high sensitivity and high selectivity. In addition, the extraordinary stability of the intramolecular duplex structure could assure a low background fluorescence at high temperature, even if the number of complementary base pairs between the substrate sequence and the enzyme sequence was reduced, allowing the sensor to work well over a wide temperature range. Similar performances of the fluorescent sensor at 4, 25 and 37°C suggested that this sensor has a good ability to resist temperature fluctuations.     

Cy5-conjugated hybridization-sensitive fluorescent oligonucleotides for ratiometric analysis of nuclear poly(A)+ RNA

Subnuclear poly(A)(+) RNA localization in living mammalian cells was visualized by ratiometric analysis using hybridization-sensitive fluorescent oligonucleotide probes. Probes were oligonucleotides, which contained a Cy5 fluorescent dye at the strand end and a thiazole orange double-labeled nucleotide inside strand. A ratiometric analysis using poly(A)-targeting probes revealed a distribution of the probe itself as red fluorescence and localization of the target RNA sequence in cell nuclei as green fluorescence. The fluorescence of the subnuclear poly(A)(+) RNA hybridized with the poly(A)-targeting probes was observed as puncta in interchromatin areas.     

Use of pteridine nucleoside analogs as hybridization probes

The pteridine nucleoside analog 3-methyl isoxanthopterin (3-MI) is highly fluorescent, with a quantum yield of 0.88, and it can be synthesized as a phosphoramidite and incorporated into oligonucleotides through a deoxyribose linkage. Within an oligonucleotide, 3-MI is intimately associated with native bases and its fluorescence is variably quenched in a sequence-dependent manner. Bend ing, annealing, binding, digestion or cleavage of fluorophore-containing oligonucleotides can be detected by monitoring changes in fluorescence properties. We developed a single step method for detecting annealing of complementary DNA sequences using 3-MI-containing oligonucleotides as hybridization probes. One of the complementary strands contains the fluorophore as an insertion and when annealing occurs, the fluorophore bulges out from the double strand, resulting in increased fluorescence intensity. We have examined the sequence dependency, optimal strand length and impact of multiple fluorophores per strand in terms of brightness and impact on the annealing process. We describe the application of this technique to the detection of positive PCR products using an HIV-1 detection system. This sequence-dependent hybridization technique can result in fluorescence intensity increases of up to 27-fold. Fluorescence intensity increases are only seen upon specific binding to bulge-generating complements, removing issues of high background from non-specific binding.     

Fluorescence detection of adenosine triphosphate through an aptamer-molecular beacon multiple probe

An aptamer-molecular beacon (MB) multiple fluorescent probe for adenosine triphosphate (ATP) assay is proposed in this article. The ATP aptamer was used as a molecular recognition part, and an oligonucleotide (short strand, SS) partially complementary with the aptamer and an MB was used as the other part. In the presence of ATP, the aptamer bound with it, accompanied by the hybridization of MB and SS and the fluorescence recovering. Wherever there is only very weak fluorescence can be measured in the absence of ATP. Based on the relationship of recovering fluorescence and the concentration of ATP, a method for quantifying ATP has been developed. The fluorescence intensity was proportional to the concentration of ATP in the range of 10 to 500 nM with a detection limit of 0.1 nM. Moreover, this method was able to detect ATP with high selectivity in the presence of guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP). This method is proved to be simple with high sensitivity, selectivity, and specificity.     

Detection of pre-mRNA splicing in vitro by an RNA-templated fluorogenic reaction

RNA splicing is an important target for basic research of disease mechanisms and for drug discovery. Here, we report a new method for analysis of the in vitro RNA splicing process that produces fluorescence using a reduction-triggered fluorescence (RETF) probe. The fluorescence signal is produced only when the two probes bind side-by-side with a specific RNA target. Precursor messenger RNA and mature messenger RNA originating from the chicken δ-crystallin (CDC) gene were successfully discriminated in solution using an RETF probe with the assistance of helper oligonucleotide strands. Also, we successfully applied RETF probes to the detection of emerging mature mRNA in an in vitro splicing process.     

Ratiometric fluorescent detection of Cu2+ based on dual‐emission ZIF‐8@rhodamine‐B nanocomposites

Zeolitic imidazolate framework‐8 (ZIF‐8) loading rhodamine‐B (ZIF‐8@rhodamine‐B) nanocomposites was proposed and used as ratiometric fluorescent sensor to detect copper(II) ion (Cu²⁺). Scanning electron microscopy, Fourier transform infrared spectroscopy, X‐ray powder diffraction, nitrogen adsorption/desorption isotherms and fluorescence emission spectroscopy were employed to characterize the ZIF‐8@rhodamine‐B nanocomposites. The results showed the rhodamine‐B was successfully assembled on ZIF‐8 based on the π‐π interaction and the hydrogen bond between the nitrogen atom of ZIF‐8 and –COOH of rhodamine‐B. The as‐obtained ZIF‐8@rhodamine‐B nanocomposites were octahedron with size about 150–200 nm, had good water dispersion, and exhibited the characteristic fluorescence emission of ZIF‐8 at 335 nm and rhodamine‐B at 575 nm. The Cu²⁺ could quench fluorescence of ZIF‐8 rather than rhodamine‐B. The ZIF‐8 not only acted as the template to assemble rhodamine‐B, but also was employed as the signal fluorescence together with the fluorescence of rhodamine‐B as the reference to construct a novel ratiometric fluorescent sensor to detect Cu²⁺. The resulted ZIF‐8@rhodamine‐B nanocomposite fluorescence probe showed good linear range (68.4 nM to 125 μM) with a low detection limit (22.8 nM) for Cu²⁺ combined with good sensitivity and selectivity. The work also provides a better way to design ratiometric fluorescent sensors from ZIF‐8 and other fluorescent molecules.     

Sensitive detection of cysteine based on fluorescent silver clusters

In this work, we report the application of novel, water-soluble fluorescent Ag clusters in fluorescent sensors for detecting cysteine, an important biological analyte. The fluorescence of poly(methacrylic acid) (PMAA)-templated Ag clusters was found to be quenched effectively by cysteine, but not when the other alpha-amino acids were present. By virtue of the specific response, a new, simple, and sensitive fluorescent method for detecting cysteine has been developed based on Ag clusters. The present assay allows for the selective determination of cysteine in the range of 2.5 x 10(-8) to 6.0 x 10(-6)M with a detection limit of 20 nM at a signal-to-noise ratio of 3. Based on the absorption and fluorescence studies, we suggested that cysteine quenched the emission by the thiol-adsorption-accelerated oxidation of the emissive Ag clusters. The present study shows a promising step toward the application of silver clusters, a new class of attractive fluorescence probes.     

Copper nanocluster‐based fluorescence enhanced determination of d‐penicillamine

Taking advantage of the compelling properties of d ‐penicillamine (d ‐PA) combined with copper, a method for the sensitive and selective determination of d ‐PA was established using copper nanocluster (Cu NC)‐based fluorescence enhancement. d ‐PA molecules containing a thiol compound showed a strong tendency to combine with the surface of Cu NCs, causing the re‐dispersion of nanoclusters and therefore fluorescence intensity was enhanced. Fluorescence enhancement efficiency of Cu NCs induced by d ‐PA was linear, with the d ‐PA concentration varying from 0.6–30 μg ml^?1 (R² = 0.9952) and with a detection limit of 0.54 μg ml^?1. d ‐PA content in human urine samples was detected with recoveries of 104.8–112.99%. Fluorescence‐enhanced determination of d ‐PA using Cu NCs was established for the first time and this rapid, easy and sensitive method should attract much attention for this application.