A novel electrochemical DNA biosensor construction based on layered CuS–graphene composite and Au nanoparticles

A novel CuS–graphene (CuS-Gr) composite was synthesized to achieve excellent electrochemical properties for application as a DNA electrochemical biosensor. CuS-Gr composite was prepared by a hydrothermal method, in which two-dimensional graphene served as a two-dimensional conductive skeleton to support CuS nanoparticles. A sensitive electrochemical DNA biosensor was fabricated by immobilizing single-stranded DNA (ss-DNA) labeled at the 5′ end using 6-mercapto-1-hexane (HS-ssDNA) on the surface of Au nanoparticles (AuNPs) to form ssDNA-S–AuNPs/CuS-Gr, and hybridization sensing was done in phosphate buffer. Cyclic voltammetry and electrochemical impedance spectroscopy were performed for the characterization of the modified electrodes. Differential pulse voltammetry was applied to monitor the DNA hybridization using an [Fe(CN)₆]^3?/4? solution as a probe. Under optimum conditions, the biosensor developed exhibited a good linear relationship between the current and the logarithm of the target DNA concentration ranging from 0.001 to 1 nM, with a low detection limit of 0.1 pM (3σ/S). The biosensor exhibited high selectivity to differentiate one-base-mismatched DNA and three-base-mismatched DNA. The results indicated that the sensing platform based on CuS-Gr provides a stable and conductive interface for electrochemical detection of DNA hybridization, and could easily be extended to the detection of other nucleic acids. Graphical abstracts

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Colorimetric detection of PCR products of DNA from pathogenic bacterial targets based on a simultaneously amplified DNAzyme

A novel strategy was devised for colorimetric analysis of the products of the polymerase chain reaction (PCR). The method takes advantage of simultaneous amplification of a horseradish peroxidase-mimicking DNAzyme (HRPzyme) during the PCR process. It is performed using a DNA specific forward primer and a universal reverse primer containing a complementary HRPzyme sequence. The double-strand PCR products, which include the HRPzyme sequence, are treated with a mixture of hemin and TMB (3,3′,5,5′–tetramethylbenzidine) in the presence of hydrogen peroxide. The resulting HRPzyme/hemin complex then promotes a peroxidase mimicking reaction, which produces the blue colored oxidized TMB. This colorimetric method can be more easily performed than previously developed gel based detection procedures and, as a result, can be conveniently applied to the specific and sensitive colorimetric analysis of DNA sequences arising from pathogenic bacteria. The potentially broad applicability of the new method has been demonstrated by its use in the identification of the 16s rDNA of Salmonella Typhimurium. Figure

A novel strategy was devised for simple colorimetric analysis of PCR products with amplification of a horseradish peroxidase-mimicking DNAzyme(HRPzyme). This colorimetric method can be much more easily performed than previously developed gel based detection procedures and potentially broad applicability for other DNA analysis.     

Fluorescent-increase kinetics of different fluorescent reporters used for qPCR depend on monitoring chemistry,targeted sequence,type of DNA input and PCR efficiency

The analysis of quantitative PCR data usually does not take into account the fact that the increase in fluorescence depends on the monitoring chemistry, the input of ds-DNA or ss-cDNA, and the directionality of the targeting of probes or primers. The monitoring chemistries currently available can be categorized into six groups: (A) DNA-binding dyes; (B) hybridization probes; (C) hydrolysis probes; (D) LUX primers; (E) hairpin primers; and (F) the QZyme system. We have determined the kinetics of the increase in fluorescence for each of these groups with respect to the input of both ds-DNA and ss-cDNA. For the latter, we also evaluated mRNA and cDNA targeting probes or primers. This analysis revealed three situations. Hydrolysis probes and LUX primers, compared to DNA-binding dyes, do not require a correction of the observed quantification cycle. Hybridization probes and hairpin primers require a correction of ?1 cycle (dubbed C-lag), while the QZyme system requires the C-lag correction and an efficiency-dependent C-shift correction. A PCR efficiency value can be derived from the relative increase in fluorescence in the exponential phase of the amplification curve for all monitoring chemistries. In case of hydrolysis probes, LUX primers and hairpin primers, however, this should be performed after cycle 12, and for the QZyme system after cycle 19, to keep the overestimation of the PCR efficiency below 0.5 %. Figure

The qPCR monitoring chemistries form six groups with distinct fluorescence kinetics. The displacement of the amplification curve depends on the chemistry, DNA input and probe-targeting. The observed shift in C_q values can be corrected and PCR efficiencies can be derived.     

Chemiluminescence microarrays in analytical chemistry: a critical review

Multi-analyte immunoassays on microarrays and on multiplex DNA microarrays have been described for quantitative analysis of small organic molecules (e.g., antibiotics, drugs of abuse, small molecule toxins), proteins (e.g., antibodies or protein toxins), and microorganisms, viruses, and eukaryotic cells. In analytical chemistry, multi-analyte detection by use of analytical microarrays has become an innovative research topic because of the possibility of generating several sets of quantitative data for different analyte classes in a short time. Chemiluminescence (CL) microarrays are powerful tools for rapid multiplex analysis of complex matrices. A wide range of applications for CL microarrays is described in the literature dealing with analytical microarrays. The motivation for this review is to summarize the current state of CL-based analytical microarrays. Combining analysis of different compound classes on CL microarrays reduces analysis time, cost of reagents, and use of laboratory space. Applications are discussed, with examples from food safety, water safety, environmental monitoring, diagnostics, forensics, toxicology, and biosecurity. The potential and limitations of research on multiplex analysis by use of CL microarrays are discussed in this review. Figure

Achievements in the development of CL microarray analysis platforms     

Carbon composite-based DNA sensor for detection of bacterial meningitis caused by Neisseria meningitidis

Carbon/1-octadecanethiol-carboxylated multiwalled carbon nanotubes (cMWCNT) composite was used to construct a DNA sensor for detection of human bacterial meningitis caused by Neisseria meningitidis. The carbon composite electrode was used to covalently immobilize 5′-amine-labeled 19-mer single-stranded DNA (ssDNA) probe, which was hybridized with 1.35?×?10²–3.44?×?10⁴ pM (0.5–128 ng/5 μl) of single-stranded genomic DNA (ssG-DNA) of N. meningitidis for 10 min at room temperature (RT). The surface topography of the DNA sensor was characterized by using scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) while electrochemically characterized by electrochemical impedance. The immobilization of ssDNA probe and hybridization with ssG-DNA were detected electrochemically by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) at RT in 30 min with a response time of 1 min. The DNA sensor showed high pathogenic specificity and can distinguish among complement, noncomplement, one base mismatch, and triple base mismatch oligomer targets. The limit of detection (LOD) and sensitivity of the sensor were approximately 68 pM and 38.095 (μA/cm²)/nM of ssG-DNA, respectively, using DPV. The improved sensitivity and LOD of the sensor can be attributed to the higher efficiency of probe immobilization due to high surface area-to-volume ratio and good electrical activity of cMWCNT. Figure

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A lipase-based electrochemical biosensor for target DNA

A lipase-based electrochemical biosensor has been fabricated for the quantitative determination of target DNA. It is based on a stem-loop nucleic acid probe labeled with ferrocene containing a butanoate ester that is hydrolyzed by lipase. The other end of the probe DNA is linked, via carboxy groups, to magnetic nanoparticles. The binding of target DNA transforms the hairpin structure of the probe DNA and causes the exposure of ester bonds. This results in the release of electro-active ferrocene after hydrolysis of the ester bonds, and in an observable electrochemical response. The quantity of target DNA in the concentration range between 1?×?10^?12 mol·L^?1 and 1?×?10^?8 mol·L^?1 can be determined by measuring the electrochemical current. The method can detect target DNA with rapid response (30 min) and low interference.

Direct electrochemistry and electrocatalysis of hemoglobin on a glassy carbon electrode modified with poly(ethylene glycol diglycidyl ether) and gold nanoparticles on a quaternized cellulose support. A sensor for hydrogen peroxide and nitric oxide

A glassy carbon electrode was modified with gold nanoparticles (Au-NPs) on a quaternized cellulose support in a film composed of poly(ethylene glycol diglycidyl ether) (PEGDGE), and Hb was immobilized on the Au-NPs. The sensor film was characterized by UV–vis spectra, scanning electron microscopy, and electrochemical impedance spectroscopy. Cyclic voltammetry of the Hb in the Au@Qc/PEGDGE film revealed a pair of well-defined and quasi reversible peaks for the protein heme Fe(III)/Fe(II) redox couple at about ?0.333 V (vs. SCE). The sensor film also exhibited good electrocatalytic activity for the reduction of nitric oxide and hydrogen peroxide. The amperometric response of the biosensor depends linearly on the concentration of nitric oxide in the 0.9 to 160 μM range, and the detection limit is as low as 12 nM (at 3σ). The response to hydrogen peroxide is linear in the 59 nM to 4.6 μM concentration range, and the detection limit is 16 nM (at 3σ). This biosensor is sensitive, reproducible, and long-term stable. Figure

An electrochemical biosensor based on the immobilization of hemoglobin in Au@Qc NPs /Poly ethylene glycol diglycidyl ether composite film is developed.     

SILAC-Pulse Proteolysis: A Mass Spectrometry-Based Method for Discovery and Cross-Validation in Proteome-Wide Studies of Ligand Binding

Reported here is the use of stable isotope labeling with amino acids in cell culture (SILAC) and pulse proteolysis (PP) for detection and quantitation of protein–ligand binding interactions on the proteomic scale. The incorporation of SILAC into PP enables the PP technique to be used for the unbiased detection and quantitation of protein–ligand binding interactions in complex biological mixtures (e.g., cell lysates) without the need for prefractionation. The SILAC-PP technique is demonstrated in two proof-of-principle experiments using proteins in a yeast cell lysate and two test ligands including a well-characterized drug, cyclosporine A (CsA), and a non-hydrolyzable adenosine triphosphate (ATP) analogue, adenylyl imidodiphosphate (AMP-PNP). The well-known tight-binding interaction between CsA and cyclophilin A was successfully detected and quantified in replicate analyses, and a total of 33 proteins from a yeast cell lysate were found to have AMP-PNP-induced stability changes. In control experiments, the method’s false positive rate of protein target discovery was found to be in the range of 2.1% to 3.6%. SILAC-PP and the previously reported stability of protein from rates of oxidation (SPROX) technique both report on the same thermodynamic properties of proteins and protein–ligand complexes. However, they employ different probes and mass spectrometry-based readouts. This creates the opportunity to cross-validate SPROX results with SILAC-PP results, and vice-versa. As part of this work, the SILAC-PP results obtained here were cross-validated with previously reported SPROX results on the same model systems to help differentiate true positives from false positives in the two experiments. Graphical Abstract

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Detection of Helicobacter pylori with a nanobiosensor based on fluorescence resonance energy transfer using CdTe quantum dots

We report on a method for the sensitive determination of Helicobacter that is based on fluorescence resonance energy transfer using two oligonucleotide probes labeled with CdTe quantum dots (QDs) and 5-carboxytetramethylrhodamine (Tamra) respectively. QDs labeled with an amino-modified first oligonucleotide, and a Tamra-labeled second oligonucleotide were added to the DNA targets upon which hybridization occurred. The resulting assembly brings the Tamra fluorophore (the acceptor) and the QDs (the donor) into close proximity and causes fluorescence resonance energy transfer (FRET) to occur upon photoexcitation of the donor. In the absence of target DNA, on the other hand, the probes are not ligated, and no emission by the Tamra fluorophore is produced due to the lack of FRET. The feasibility of the method was demonstrated by the detection of a synthetic 210-mer nucleotide derived from Helicobacter on a nanomolar level. This homogeneous DNA detection scheme is simple, rapid and efficient, does not require excessive washing and separation steps, and is likely to be useful for the construction of a nanobiosensor for Helicobacter species.

Prussian blue-doped nanogold microspheres for enzyme-free electrocatalytic immunoassay of p53 protein

We report on a new enzyme-free electrochemical immunoassay for the sensitive detection of the p53 protein (p53; a model analyte) by using a screen-printed carbon electrode modified with monoclonal mouse anti-human p53 antibody tagged with gold nanoparticles. First, nanogold microspheres doped with Prussian Blue were synthesized by a reverse micelle method. The resulting microspheres were used to label polyclonal anti-p53 antibody which then was applied in a sandwich immunoassay in pH 6.5 buffer solution using the Prussian Blue in the particles as the redox-active reporter. The electrochemical signal of the immunosensor is shown to increase with the concentration of the analyte (p53 protein) in the range from 0.5 to 80 U mL^?1, with a detection limit of 0.1 U mL^?1. No non-specific adsorption was observed. Coefficients of variation for intra-assay and inter-assay were below 8.5 % and 11.5 %, respectively. In addition, the method was applied to the analysis of 15 human serum samples, and a good relationship was found between the new immunoassay and the referenced electro-chemiluminescence method.

CdS quantum dots as a fluorescent sensing platform for nucleic acid detection

We demonstrate that CdS quantum dots (QDs) can be applied to fluorescence-enhanced detection of nucleic acids in a two-step protocol. In step one, a fluorescently labeled single-stranded DNA probe is adsorbed on the QDs to quench its luminescence. In step two, the hybridization of the probe with its target ssDNA produces a double-stranded DNA which detaches from the QD. This, in turn, leads to the recovery of the fluorescence of the label. The lower detection limit of the assay is as low as 1?nM. The scheme (that was applied to detect a target DNA related to the HIV) is simple and can differentiate between perfectly complementary targets and mismatches.

Direct electrochemistry of glucose oxidase and a biosensor for glucose based on a glass carbon electrode modified with MoS2 nanosheets decorated with gold nanoparticles

An electrochemical glucose biosensor was developed by immobilizing glucose oxidase (GOx) on a glass carbon electrode that was modified with molybdenum disulfide (MoS₂) nanosheets that were decorated with gold nanoparticles (AuNPs). The electrochemical performance of the modified electrode was investigated by cyclic voltammetry, and it is found that use of the AuNPs-decorated MoS₂ nanocomposite accelerates the electron transfer from electrode to the immobilized enzyme. This enables the direct electrochemistry of GOx without any electron mediator. The synergistic effect the MoS₂ nanosheets and the AuNPs result in excellent electrocatalytic activity. Glucose can be detected in the concentration range from 10 to 300 μM, and down to levels as low as 2.8 μM. The biosensor also displays good reproducibility and long-term stability, suggesting that it represents a promising tool for biological assays. Figure

A MoS₂-based glucose sensor has been prepared by gold nanoparticles-decorated MoS₂ nanocomposite, which exhibited excellent electrocatalytic activity, reproducibility and long-term stability. It was applied to determine glucose concentration in human serum, suggest the sensor maybe promising for practical application.     

Enzyme-linked electrochemical DNA ligation assay using magnetic beads

DNA ligases are essential enzymes in all cells and have been proposed as targets for novel antibiotics. Efficient DNA ligase activity assays are thus required for applications in biomedical research. Here we present an enzyme-linked electrochemical assay based on two terminally tagged probes forming a nicked junction upon hybridization with a template DNA. Nicked DNA bearing a 5' biotin tag is immobilized on the surface of streptavidin-coated magnetic beads, and ligated product is detected via a 3' digoxigenin tag recognized by monoclonal antibody-alkaline phosphatase conjugate. Enzymatic conversion of napht-1-yl phosphate to napht-1-ol enables sensitive detection of the voltammetric signal on a pyrolytic graphite electrode. The technique was tested under optimal conditions and various situations limiting or precluding the ligation reaction (such as DNA substrates lacking 5′-phosphate or containing a base mismatch at the nick junction, or application of incompatible cofactor), and utilized for the analysis of the nick-joining activity of a range of recombinant Escherichia coli DNA ligase constructs. The novel technique provides a fast, versatile, specific, and sensitive electrochemical assay of DNA ligase activity.

Exonuclease I aided enzyme-linked aptamer assay for small-molecule detection

A novel enzyme-linked aptamer assay (ELAA) with the aid of Exonuclease I (Exo I) for colorimetric detection of small molecules was developed. The fluorescein isothiocyanate (FITC)-labeled aptamer was integrated into a double-stranded DNA (dsDNA). In the presence of target, the binding of aptamer with target protected the aptamer from Exo I degradation, which resulted in the FITC tag remaining on the aptamer. Then, the anti-FITC-HRP conjugate was used to produce an optically observable signal. By monitoring the color change, we were able to detect two model molecules, ATP and L-argininamide, with high selectivity and high sensitivity even in the serum matrix. It is expected to be a simple and general ELAA method with wide applicability.

Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens

We report on the development of an on-chip RPA (recombinase polymerase amplification) with simultaneous multiplex isothermal amplification and detection on a solid surface. The isothermal RPA was applied to amplify specific target sequences from the pathogens Neisseria gonorrhoeae, Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA) using genomic DNA. Additionally, a positive plasmid control was established as an internal control. The four targets were amplified simultaneously in a quadruplex reaction. The amplicon is labeled during on-chip RPA by reverse oligonucleotide primers coupled to a fluorophore. Both amplification and spatially resolved signal generation take place on immobilized forward primers bount to expoxy-silanized glass surfaces in a pump-driven hybridization chamber. The combination of microarray technology and sensitive isothermal nucleic acid amplification at 38 °C allows for a multiparameter analysis on a rather small area. The on-chip RPA was characterized in terms of reaction time, sensitivity and inhibitory conditions. A successful enzymatic reaction is completed in <20 min and results in detection limits of 10 colony-forming units for methicillin-resistant Staphylococcus aureus and Salmonella enterica and 100 colony-forming units for Neisseria gonorrhoeae. The results show this method to be useful with respect to point-of-care testing and to enable simplified and miniaturized nucleic acid-based diagnostics. Figure

The combination of multiplex isothermal nucleic acid amplification with RPA and spatially-resolved signal generation on specific immobilized oligonucleotides     

A turn-on fluorescence-sensing technique for glucose determination based on graphene oxide–DNA interaction

Graphene is a two-dimensional carbon nanomaterial one atom thick. Interactions between graphene oxide (GO) and ssDNA containing different numbers of bases have been proved to be remarkably different. In this paper we propose a novel approach for turn-on fluorescence sensing determination of glucose. Hydrogen peroxide (H₂O₂) is produced by glucose oxidase-catalysed oxidation of glucose. In the presence of ferrous iron (Fe²⁺) the hydroxyl radical (?OH) is generated from H₂O₂ by the Fenton reaction. This attacks FAM-labelled long ssDNA causing irreversible cleavage, as a result of the oxidative effect of ?OH, producing an FAM-linked DNA fragment. Because of the weak interaction between GO and short FAM-linked DNA fragments, restoration of DNA fluorescence can be achieved by addition of glucose. Due to the excellent fluorescence quenching efficiency of GO and the specific catalysis of glucose oxidase, the sensitivity and selectivity of this method for GO-DNA sensing are extremely high. The linear range is from 0.5 to 10 μmol L^?1 and the detection limit for glucose is 0.1 μmol L^?1. The method has been successfully used for analysis of glucose in human serum. Figure

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Metal-nanoparticle-involved chemiluminescence and its applications in bioassays

Chemiluminescence-based bioassays have become increasingly important in clinical, pharmaceutical, environmental, and food safety fields owing to their high sensitivity, wide linear range, and simple instrumentation. During the past decade, it has been found that metal nanoparticles can initiate various liquid-phase chemiluminescence reactions as catalysts, reductants, energy acceptors, and nanosized reaction platforms owing to their unique optical, catalytic, and surface properties and chemical reactivity, which are very important for chemiluminescence bioassays based on metal nanoparticles as nanoprobes or a nanointerface. In this article, we summarize recent progress in metal-nanoparticle-initiated liquid-phase chemiluminescence, including reaction systems, mechanisms, and their applications in chemiluminescence-based bioassays, especially for immunoassays, DNA assays, aptamer-based assays, high-performance liquid chromatography or capillary electrophoresis analysis, and flow injection analysis. Figure

Comprehensive summary of metal nanoparticle (NP)-involved chemiluminescence (CL) systems and their applications. CE capillary electrophoresis, HPLC highperformance liquid chromatography     

Initial Velocity Distribution of MALDI/LDI Ions Measured by Internal MALDI Source Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry

A new method for measuring the ion velocity distribution using an internal matrix-assisted laser desorption/ionization (MALDI) source Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer is described. The method provides the possibility of studying ion velocities without any influence of electric fields in the direction of the instrument axis until the ions reach the ICR cell. It also allows to simultaneously account for and to estimate not only the velocity distribution but the angular distribution as well. The method was demonstrated using several types of compounds in laser desorption/ionization (LDI) mode. Graphical Abstract

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On-site detection of Phytophthora spp.—single-stranded target DNA as the limiting factor to improve on-chip hybridization

We report on a lab-on-a-chip approach for on-site detection of Phytophthora species that allows visual signal readout. The results demonstrate the significance of single-stranded DNA (ssDNA) generation in terms of improving the intensity of the hybridization signal and to improve the reliability of the method. Conventional PCR with subsequent heat denaturation, sodium hydroxide-based denaturation, lambda exonuclease digestion and two asymmetric PCR methods were investigated for the species P. fragariae, P. kernoviae, and P. ramorum. The positioning of the capture probe within the amplified yeast GTP-binding protein (YPT1) target DNA was also of interest because it significantly influences the intensity of the signal. Statistical tests were used to validate the impact of the ssDNA generation methods and the capture-target probe position. The single-stranded target DNA generated by Linear-After-The-Exponential PCR (LATE-PCR) was found to produce signal intensities comparable to post-PCR exonuclease treatment. The LATE-PCR is the best method for the on-site detection of Phytophthora because the enzymatic digestion after PCR is more laborious and time-consuming. Figure

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