One-step synthesized silver micro-dendrites used as novel separation mediums and their applications in multi-DNA analysis

A new kind of silver micro-dendrites have been synthesized for the separation and multiplex detection of DNA merely by earth gravity. Through this approach, the DNA strands of the sickle cell disease, human T-lymphotropic virus type I, the anthrax lethal factor can be detected down to 100 pM with the detection range from 100 pM to 100 nM at the same time.     

Electrochemical DNA sensor by the assembly of graphene and DNA-conjugated gold nanoparticles with silver enhancement strategy

Sensitive and selective detection of DNA is in urgent need due to its important role in human bodies. Many disorders, such as Alzheimer's disease and various cancers, are closely related with DNA damage. In this work, a novel electrochemical DNA biosensor was constructed on a DNA-assembling graphene platform which provided a robust, simple and biocompatible platform with large surface area for DNA immobilization. The as-designed DNA sensor was fabricated by directly assembling captured ssDNA on a graphene-modified electrode through the π-π stacking interaction between graphene and ssDNA bases. Then, the target DNA sequence and oligonucleotide probes-labeled AuNPs were able to hybridize in a sandwich assay format, following the AuNPs-catalyzed silver deposition. The deposited silver was further detected by differential pulse voltammetry. Owing to the high DNA loading ability of graphene and the distinct signal amplification by AuNPs-catalyzed silver staining, the resulting biosensor exhibited a good analytical performance with a wide detection linear range from 200 pM to 500 nM, and a low detection limit of 72 pM. Additionally, the biosensor was proved to be able to discriminate the complementary sequence from the single-base mismatch sequence. The simple biosensor is promising in developing electronic, on-chip assays in clinical diagnosis, environmental control, and drug discovery.     

Synthesis of length-controlled polyvalent silver nanowire-DNA conjugates for sensitive and selective detection of DNA targets

We have developed a facile method to rapidly synthesize the monodisperse silver nanowire-DNA conjugates with a constant diameter and systematically controllable lengths in the range of 0.5-2.5 μm. The synthesis of silver nanowires takes advantage of poly(sodium 4-styrenesulfonate) as a structure-directing reagent and is performed under very mild conditions such as room temperature and aqueous media. The nanowires are densely conjugated with DNA sequences enough to exhibit the cooperative properties for the sensitive and selective detection of DNA targets. The limit of detection is 50 pM.     

Development of a photodiode array biochip using a bipolar semiconductor and its application to detection of human papilloma virus

We describe a DNA microarray system using a bipolar integrated circuit photodiode array (PDA) chip as a new platform for DNA analysis. The PDA chip comprises an 8 × 6 array of photodiodes each with a diameter of 600 μm. Each photodiode element acts both as a support for an immobilizing probe DNA and as a two-dimensional photodetector. The usefulness of the PDA microarray platform is demonstrated by the detection of high-risk subtypes of human papilloma virus (HPV). The polymerase chain reaction (PCR)-amplified biotinylated HPV target DNA was hybridized with the immobilized probe DNA on the photodiode surface, and the chip was incubated in an anti-biotin antibody-conjugated gold nanoparticle solution. The silver enhancement by the gold nanoparticles bound to the biotin of the HPV target DNA precipitates silver metal particles at the chip surfaces, which block light irradiated from above. The resulting drop in output voltage depends on the amount of target DNA present in the sample solution, which allows the specific detection and the quantitative analysis of the complementary target DNA. The PDA chip showed high relative signal ratios of HPV probe DNA hybridized with complementary target DNA, indicating an excellent capability in discriminating HPV subtypes. The detection limit for the HPV target DNA analysis improved from 1.2 nM to 30 pM by changing the silver development time from 5 to 10 min. Moreover, the enhanced silver development promoted by the gold nanoparticles could be applied to a broader range of target DNA concentration by controlling the silver development time. Figure An optical image of the PDA chip and target DNA detection through silver enhancement Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of glutathione by voltammetric analysis with rolling circle amplification

Glutathione (GSH), a common tripeptide, plays an essential role in a variety of cellular functions. GSH level is reported to be closely related to human health. In this study, we fabricate an ultrasensitive electrochemical biosensor for GSH quantification. DNA probes are firstly modified on the electrode surface and thymine-Hg²⁺-thymine is formed. Since GSH is able to chelate Hg²⁺ from the DNA mismatched sites effectively, which leads to DNA structural switching from hairpin to linear strand, rolling circle amplification (RCA) could be initiated with the released linear primer probe. The RCA product with multiple repeating sequences further captures numerous DNA modified silver nanoparticles (AgNPs) by the hybridization of complementary sequences. Stripping voltammetric responses of AgNPs are then detected to reveal GSH concentration. The linear detection range is from 0.1 pM to 10 nM and the limit of detection is 0.1 pM, which is lower than most current analytical methods. This method is also highly selective and functions well against a series of interferents. Additionally, the proposed method has been successfully utilized in human serum samples, which shows fairly good potential in clinical applications.     

Ultratrace voltammetric method for the detection of DNA sequence related to human immunodeficiency virus type 1

An ultra-trace voltammetric method was developed for the determination of single strand DNA (ss-DNA) related to the human immunodeficiency virus type 1 (HIV-1). It is based on the signal amplification of carbon nanotubes loaded with silver nanoparticles and placed on a gold microelectrode. The capture ss-DNA (a 21-mer) possessing a thiol group at the 3?? end was self-assembled onto the surface of the gold microelectrode. It was then hybridized with target HIV-1 ss-DNA (a 42-mer) and further hybridized with the electrochemical probe (a 18-mer ss-DNA) tagged with multiwall carbon nanotubes and loaded with silver nanoparticles. The resulting formation of a DNA sandwich conjugate led to a strong electrochemical oxidation signal that was linearly proportional to the concentration of HIV-1 ss-DNA in the range from 1.0 to 100?pM. The detection limit was 0.5?pM (at an S/N of 3). This was equivalent to 0.05?fmol of HIV-1 ss-DNA in a volume of 20???L. The relative standard deviation was 4.0% at 1.0?pM (n?=?11). Non-complementary ss-DNA of HIV-1 ss-DNA was effectively discriminated. This work demonstrates that the employment of the microelectrode and a sandwich hybridization model is promising in terms of sensitive and selective electrochemical detection of DNA.

Study of Bare and Mercury‐Coated Vibrated Carbon,Gold and Silver Microwire Electrodes for the Determination of Lead and Cadmium in Seawater by Anodic Stripping Voltammetry

Carbon, gold and silver microwires are revisited under vibrated conditions for detection of trace lead and cadmium in seawater. The Pb and Cd peaks fully overlapped on the bare gold and carbon electrodes and partially on the silver electrode. The sensitivity of all three was insufficient for detection in uncontaminated waters. Peak separation was obtained after coating with mercury (Hg). Only the Hg‐coated silver electrode is suitable when preplated. Limits of detection for Pb using the Hg/C and Hg/Ag electrodes (20–40 pM), and Cd (70 pM), are sufficiently low for Pb and Cd detection in seawater.     

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.

Target-driven self-assembly of stacking deoxyribonucleic acids for highly sensitive assay of proteins

In this paper, we report a new signal amplification strategy for highly sensitive and enzyme-free method to assay proteins based on the target-driven self-assembly of stacking deoxyribonucleic acids (DNA) on an electrode surface. In the sensing procedure, binding of target protein with the aptamer probe is used as a starting point for a scheduled cycle of DNA hairpin assembly, which consists of hybridization, displacement and target regeneration. Following numbers of the assembly repeats, a great deal of DNA duplexes can accordingly be formed on the electrode surface, and then switch on a succeeding propagation of self-assembled DNA concatemers that provide further signal enhancement. In this way, each target binding event can bring out two cascaded DNA self-assembly processes, namely, stacking DNA self-assembly, and therefore can be converted into remarkably intensified electrochemical signals by associating with silver nanoparticle-based readout. Consequently, highly sensitive detection of target proteins can be achieved. Using interferon-gamma as a model, the assay method displays a linear range from 1 to 500 pM with a detection limit of 0.57 pM, which is comparable or even superior to other reported amplified assays. Moreover, the proposed method eliminates the involvement of any enzymes, thereby enhancing the feasibility in clinical diagnosis.     

Studies of the interaction of two organophosphonates with nanostructured silver surfaces

Electrochemical cycling of silver surfaces in the presence of the organophosphonates paraoxon and malathion leads to changes in the electrochemical response of silver and the formation of silver nanostructures. Adsorption of the organophosphonates onto the silver surfaces causes a significant reduction in the observed current response due to an increase in the charge transfer resistance. Surface enhanced Raman spectroscopy (SERS) measurements indicate that paraoxon adsorbs with no structural changes, while malathion decomposes and a thiophosphonate interacts with the surface. The SERS study of these adsorbates was carried out by changing the electrochemical conditions and the concentration of the organophosphonates. The size of the nanostructures greatly influences the SERS signal and it is observed that the strongest enhancement is observed for mid-sized nanostructures with a uniform thickness on the surface. The limit of detection was shown to be in the range of 10 nM to 10 pM for paraoxon and malathion, respectively.     

Comparative microRNA detection from precursor-microRNA-transfected hepatocellular carcinoma cells by capillary electrophoresis with dual-color laser-induced fluorescence

A dual-LIF (dLIF) setup combined with CE for microRNA (miRNA) detection is proposed in this study. An argon ion laser (488 nm) and a solid state laser (640 nm) were chosen to excite the fluorescent dye-labeled DNA probe after splinted ligation of miRNA. The crosstalk of emission spectrum of Alex Fluor 488 and Alex Fluor 647 is minimized with a zero crosstalk matrix for Alex Fluor 647 to 488 channels. The linear ranges of the device for the fluorescent dye-labeled DNA probe were both from 1.0 nM to 0.1 pM. The limits of detection for Alexa Fluor 488-labeled DNA and Alex Fluor 647-labeled DNA were 9.3 and 31 fM, respectively. The detection of specific miRNA has been accomplished by combining splinted ligation with the fluorescent dye-labeled oligonucleotides. The linear range for the synthetic miRNA is from 1.0 nM to 1.0 pM. Without PCR amplification, CE-dLIF was applied to discriminate a pre-miR-10b*-transfected cells (contains precursor miR-10b*) from hepatocellular carcinoma cell (control cells). Therefore, this result indicates CE-dLIF has great potential to provide a rapid comparative assay for miRNAs detection.     

A New Route for the Enzymeless Trace Level Detection of Creatinine Based on Reduced Graphene Oxide/Silver Nanocomposite Biosensor

Renal insufficiencies and muscle diseases can be easily identified from the concentration of creatinine in blood and urine. Although various chemical sensors have been developed to detect creatinine, selectivity and robustness of chemical sensors are the main obstacles for many researchers. To overcome these difficulties, finding a suitable chemical biosensor with long‐term stability, low cost, high sensitivity and selectivity for the detection of creatinine is immensely desirable. Herein, we have developed a novel enzymeless creatinine biosensor for the trace level detection of creatinine using reduced graphene oxide (RGO)/ silver nanoparticles (AgNPs) which was prepared by simple one step electrochemical potentiodyanamic method. The anodic peak current of AgNPs gradually decreased when the concentration of creatinine was increased. Based on the decrease of anodic peak current, we have introduced a new platform for the detection of creatinine. The adsorption of creatinine on AgNPs was confirmed by various techniques. The newly proposed biosensor exhibited a very low detection limit of 0.743 pM with linear range from 10 pM to 120 pM. The demonstrated sensor can detect creatinine even in the presence of other interfering biomolecules such as glucose, ascorbic acid, uric acid, urea and creatine.     

Label-free genotyping of cytochrome P450 2D6*10 using ligation-mediated strand displacement amplification with DNAzyme-based chemiluminescence detection

Genotyping of cytochrome P450 monooxygenase 2D6*10 (CYP2D6*10) plays an important role in pharmacogenomics, especially in clinical drug therapy of Asian populations. This work reported a novel label-free technique for genotyping of CYP2D6*10 based on ligation-mediated strand displacement amplification (SDA) with DNAzyme-based chemiluminescence detection. Discrimination of single-base mismatch is firstly accomplished using DNA ligase to generate a ligation product. The ligated product then initiates a SDA reaction to produce aptamer sequences against hemin, which can be probed by chemiluminescence detection. The proposed strategy is used for the assay of CYP2D6*10 target and the genomic DNA. The results reveal that the proposed technique displays chemiluminescence responses in linear correlation to the concentrations of DNA target within the range from 1 pM to 1 nM. A detection limit of 0.1 pM and a signal-to-background ratio of 57 are achieved. Besides such high sensitivity, the proposed CYP2D6*10 genotyping strategy also offers superb selectivity, great robustness, low cost and simplified operations due to its label-free, homogeneous, and chemiluminescence-based detection format. These advantages suggest this technique may hold considerable potential for clinical CYP2D6*10 genotyping and association studies.     

Electrochemical Detection of DNA Hybridization Based on the Probe Labeled with Carbon‐Nanotubes Loaded with Silver Nanoparticles

A sensitive electrochemical method for the detection of DNA hybridization based on the probe labeled with multiwall carbon‐nanotubes (MWNTs) loaded with silver nanoparticles (Ag‐MWNTs) has been developed. MWNTs were electroless‐plated with a large number of silver nanoparticles to form Ag‐MWNTs. Probe single strand DNA (ss‐DNA) with a thiol group at the 3′‐terminal labeled with Ag‐MWNTs by self‐assembled monolayer (SAM) technique was employed as an electrochemical probe. Target ss‐DNA with a thiol group was immobilized on a gold electrode by SAM technique and then hybridized with the electrochemical probe. Binding events were monitored by differential pulse voltammetric (DPV) signal of silver nanoparticles. The signal difference permitted to distinguish the match of two perfectly complementary DNA strands from the near perfect match where just three base pairs were mismatched. There was a linear relation between the peak current at +120 mV (vs. SCE) and complementary target ss‐DNA concentration over the range from 3.1×10^?14 to 1.0×10^?11 mol/L with a detection limit of 10 fmol/L of complementary target ss‐DNA. The proposed method has been successfully applied to detection of the DNA sequence related to cystic fibrosis. This work demonstrated that the MWNTs loaded with silver nanoparticles offers a great promising approach for sensitive detection of DNA hybridization.     

Gold nanoparticle aggregation-based highly sensitive DNA detection using atomic force microscopy

The potential ability of atomic force microscopy (AFM) as a quantitative bioanalysis tool is demonstrated by using gold nanoparticles as a size enhancer in a DNA hybridization reaction. Two sets of probe DNA were functionalized on gold nanoparticles and sandwich hybridization occurred between two probe DNAs and target DNA, resulting in aggregation of the nanoparticles. At high concentrations of target DNA in the range from 100 nM to 10 μM, the aggregation of gold nanoparticles was determined by monitoring the color change with UV-vis spectroscopy. The absorption spectra broadened after the exposure of DNA–gold nanoparticles to target DNA and a new absorption band at wavelengths >600 nm was observed. However, no differences were observed in the absorption spectra of the gold nanoparticles at low concentrations of target DNA (10 pM to 10 nM) due to insufficient aggregation. AFM was used as a biosensing tool over this range of target DNA concentrations in order to monitor the aggregation of gold nanoparticles and to quantify the concentration of target DNA. Based on the AFM images, we successfully evaluated particle number and size at low concentrations of target DNA. The calibration curve obtained when mean particle aggregate diameter was plotted against concentration of target DNA showed good linearity over the range 10 pM to 10 nM, the working range for quantitative target DNA analysis. This AFM-based DNA detection technique was three orders of magnitude more sensitive than a DNA detection method based on UV-vis spectroscopy.     

Colorimetric detection of DNA by modulation of thrombin activity on gold nanoparticles

A colorimetric, non-cross-linking aggregation-based gold-nanoparticle (AuNP) probe has been developed for the detection of DNA and the analysis of single-nucleotide polymorphism (SNP). The probe acts by modulating the enzyme activity of thrombin relative to fibrinogen. A thrombin-binding aptamer with a 29-base-long oligonucleotide (TBA(29)) assembled on the nanoparticles (TBA(29)-AuNPs) through sandwich DNA hybridization was found to possess ultra-high anticoagulant potency. The enzyme inhibition of thrombin was determined by thrombin-induced aggregation of fibrinogen-functionalized 56 nm AuNPs (Fib-AuNPs). The potency of the inhibition of TBA(29)-AuNPs relative to thrombin--and thus the degree of aggregation of the Fib-AuNPs--is highly dependent on the concentration of perfectly matched DNA (DNA(pm)). Under optimal conditions [Tris-HCl (20 mM, pH 7.4), KCl (5 mM), MgCl(2) (1 mM), CaCl(2) (1 mM), NaCl (150 mM), thrombin (10 pM), and TBA(29)-AuNPs (20 pM)], the new TBA(29)-AuNP/Fib-AuNP probe shows linear sensitivity to DNA(pm) in the concentration range 20-500 pM with a correlation coefficient of 0.96. The limit of detection for DNA(pm) was experimentally determined to be 12 pM, based on a signal-to-noise ratio (S/N) of 3. The new probe was successfully applied to the analysis of an SNP that is responsible for sickle cell anemia. Relative to conventional molecular-beacon-based probes, the new probe offers the advantages of higher sensitivity and selectivity towards DNA and lower cost, showing its great potential for practical studies of SNPs.     

Triple Amplification Strategy for the Improved Efficiency of a Microplate-Based Assay for the Chemiluminescent Detection of DNA

Significant research efforts are currently focused on advancing DNA detection methodology. Various nanoparticles (NPs), which are currently the most widely used solid-phase carriers for nucleic acid assays, have a number of essential drawbacks. Microtiter plates provide a simple and economical alternative to the NPs. This article reports the development of a sandwich assay for DNA detection using a microtiter plate as the solid carrier. A capture oligonucleotide modified with fluorescein was bound to the anti-fluorescein antibody adsorbed on the polystyrene microplate surface. A hepatitis B virus DNA fragment was used as the model analyte. To improve the assay sensitivity, the biotinylated reporter oligonucleotide and streptavidin-horseradish polyperoxidase (polyHRP) conjugate were used to provide an amplified detection system. Additional amplification was achieved because the peroxidase activity was measured by a chemiluminescent method using the 3-(10′-phenothiazinyl)propane-1-sulfonate/N-morpholinopyridine pair as an enhancing reagent. The detection limit of the developed assay was 0.9?pM with a linear dynamic range from 0.9 to 100?pM. This method may be used as a platform for the development of sensitive DNA assays.     

Increased intensities of YOYO-1-labeled DNA oligomers near silver particles

DNA detection is usually performed using fluorescence probes. Using a DNA oligomer stained with the widely used dye 1,1'-[1,3-propanediylbis[(dimethylimino)-3,1-propanediyl]]bis[4-[(3-methyl-2(3H)-benzoxazolylidene)methyl]]-quinolinum tetraiodide (YOYO-1), we show that a substrate containing silver particles can lead to a greater than 10-fold increase in the fluorescence intensity. Proximity to silver particles also increases the photostability of YOYO-1-DNA. These results suggest that substrates or gels containing silver particles may be used for increased sensitivity in DNA detection.     

Three different signal amplification strategies for the impedimetric sandwich detection of thrombin

In this work, we report a comparative study on three highly specific amplification strategies for the ultrasensitive detection of thrombin with the use of aptamer sandwich protocol. The protocol consisted on the use of a first thrombin aptamer immobilized on the electrode surface, the recognition of thrombin protein, and the reaction with a second biotinylated thrombin aptamer forming the sandwich. Through the exposed biotin end, three variants have been tested to amplify the electrochemical impedance signal. The strategies included (a) silver enhancement treatment, (b) gold enhancement treatment and (c) insoluble product produced by the combination of the enzyme horseradish peroxidase (HRP) and 3-amino-9-ethylcarbazole (AEC). The properties of the sensing surface were probed by electrochemical impedance measurements in the presence of the ferrocyanide/ferricyanide redox marker. Insoluble product strategy and silver enhancement treatment resulted in the lowest detection limit (0.3 pM), while gold enhancement method resulted in the highest reproducibility, 8.8% RSD at the pM thrombin concentration levels. Results of silver and gold enhancement treatment also permitted direct inspection by scanning electron microscopy (SEM).     

Coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites for the detection of BCR/ABL fusion gene

This article described a novel method by coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites (GS/PANI/AuNPs) for highly sensitive and specific detection of BCR/ABL fusion gene (bcr/abl) in chronic myeloid leukemia (CML). DNA circuit known as catalyzed hairpin assembly (CHA) is enzyme-free and can be simply operated to achieve exponential amplification, which has been widely employed in biosensing. However, application of CHA has been hindered by the need of specially redesigned sequences for each single-stranded DNA input. Herein, a transducer hairpin (HP) was designed to obtain a universal DNA circuit with favorable signal-to-background ratio. To further improve signal amplification, GS/PANI/AuNPs with excellent conductivity and enlarged effective area were introduced into this DNA circuit. Consequently, by combining the advantages of CHA and GS/PANI/AuNPs, bcr/abl could be detected in a linear range from 10 pM to 20 nM with a detection limit of 1.05 pM. Moreover, this protocol showed excellent specificity, good stability and was successfully applied for the detection of real sample, which demonstrated its great potential in clinical application.