Femtomolar electrochemical detection of DNA targets using metal sulfide nanoparticles

A new electrochemical DNA sensor providing detection capabilities down to 100 attomol of target DNA has been developed. The method applies CdS, ZnS, and PbS nanoparticles conjugated with short DNA sequences which are immobilized via hybridization with complementary sequences on a gold surface. When the DNA target is added, it can be identified by ousting the existing hybridization between one of the DNA-nanoparticle conjugates and the surface DNA. The nanoparticles remaining at the surface are detected by stripping voltammetry. The setup is constructed to give a signal-off response with a build-in control signal as only one of two different metal sulfide signaling probes on the surface is removed by hybridization with the DNA target. The competition assay is, in principle, label-free since no labels are required for detection after addition of DNA target. The dissociation of PbS nanoparticles from the surface after addition of the DNA target has been imaged by fluid phase AFM.     

Biosensor for multiplex detection of two DNA target sequences using enzyme-functionalized Au nanoparticles as signal amplification

Multiplex electrochemical detection of two DNA target sequences in one sample using enzyme-functionalized Au nanoparticles (AuNPs) as catalytic labels for was proposed. This DNA sensor was fabricated using a “sandwich” detection strategy, involving two kinds of capture probes DNA immobilized on glassy carbon electrode (GCE), and hybridization with target DNA sequences, which further hybridized with the reporter DNA loaded on the AuNPs. The AuNP contained two kinds of DNA sequences, one was complementary to the target DNA, while the other was noncomplementary to the target. The noncomplementary sequences were linked with horseradish peroxidase (HRP) and alkaline phosphatase (ALP), respectively. Enhanced detection sensitivity was obtained where the AuNPs carriers increased the amount of enzyme molecules per hybridization. Electrochemical signals were generated from the enzymatic products produced from the substrates catalyzed by HRP and ALP. Under optimal conditions, a 33-mer sequence could be quantified over the ranges from 1.5 × 10⁻¹³ to 5.0 × 10⁻¹² M with a detection limit of 1.0 × 10⁻¹³ M using HRP-AuNP as labels, and a 33-mer sequence could be quantified over the ranges from 4.5 × 10⁻¹¹ M to 1.0 × 10⁻⁹ M with a detection limit of 1.2 × 10⁻¹¹ M using ALP-AuNP as labels.     

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.

Nanoporous Ge coated by Au nanoparticles for electrochemical application

We present an innovative device based on a nanoporous Ge electrode decorated by gold nanoparticles (AuNPs). A study aimed at obtaining the best AuNP deposition conditions, which allow the decoration of Ge walls with AuNPs, avoiding particles aggregation is reported.The performance of the electrode has been evaluated by the electrocatalytic reduction of iodoethane in acetonitrile solution, a model reaction in organic electrocatalysis.     

Magnetically trigged direct electrochemical detection of DNA hybridization using Au67 quantum dot as electrical tracer

A novel gold nanoparticle-based protocol for detection of DNA hybridization based on a magnetically trigged direct electrochemical detection of gold quantum dot tracers is described. It relies on binding target DNA (here called DNA1) with Au(67) quantum dot in a ratio 1:1, followed by a genomagnetic hybridization assay between Au(67)-DNA1 and complementary probe DNA (here called DNA2) marked paramagnetic beads. Differential pulse voltammetry is used for a direct voltammetric detection of resulting Au(67) quantum dot-DNA1/DNA2-paramagnetic bead conjugate on magnetic graphite-epoxy composite electrode. The characterization, optimization, and advantages of the direct electrochemical detection assay for target DNA are demonstrated. The two main highlights of presented assay are (1) the direct voltammetric detection of metal quantum dots obviates their chemical dissolution and (2) the Au(67) quantum dot-DNA1/DNA2-paramagnetic bead conjugate does not create the interconnected three-dimensional network of Au-DNA duplex-paramagnetic beads as previously developed nanoparticle DNA assays, pushing down the achievable detection limits.     

High-performance liquid chromatographic assay for mitoxantrone in plasma using electrochemical detection

A sensitive and specific high-performance liquid chromatographic (HPLC) assay was developed for the quantitation of mitoxantrone in plasma using electrochemical detection. Bisantrene was chosen as the internal standard. A reversed-phase, 10-microns muBondapak C18 analytical column (30 cm X 3.9 mm) with an isocratic mobile phase of 28% acetonitrile in 80 mM sodium formate buffer (pH 3.0) was used. The eluent was monitored by both electrochemical detection at an applied potential of +0.75 V vs. Ag/AgCl and visible absorbance at 660 nm. Only electrochemical detection was able to quantitate the internal standard and provided ten times higher sensitivity than visible absorbance for mitoxantrone with a detection limit as low as 0.1 ng/ml. Calibration curves in the range 0.1-1000 ng/ml showed good linearity (r = 0.998) and precision (coefficient of variation less than 10%). This HPLC method utilized a reproducible and inexpensive liquid-liquid extraction procedure. Using methylene chloride, the extraction efficacy of mitoxantrone from plasma was 85.3% with a coefficient of variation less than 2.1%. This new assay was then applied to measure mitoxantrone concentrations in plasma obtained from two leukemic patients receiving 12 mg/m2 mitoxantrone as a 1-h infusion.     

Microplate electrochemical DNA detection for phosphinothricin acetyltransferase gene sequence with cadmium sulfide nanoparticles

An electrochemical DNA detection method for the phosphinothricin acetyltransferase (PAT) gene sequence from the transgenetic plants was established by using a microplate hybridization assay with cadmium sulfide (CdS) nanoparticles as oligonucleotides label. The experiment included the following procedures. Firstly target PAT ssDNA sequences were immobilized on the polystyrene microplate by physical adsorption. Then CdS nanoparticle labeled oligonucleotide probes were added into the microplate and the hybridization reaction with target ssDNA sequences took place in the microplate. After washing the microplate for three times, certain amounts of HNO₃ were added into the microplate to dissolve the CdS nanoparticles anchored on the hybrids and a solution containing Cd²⁺ ion was obtained. At last differential pulse anodic stripping voltammetry (DPASV) was used for the sensitive detection of released Cd²⁺ ion. Based on this principle a sensitive electrochemical method for the PAT gene sequences detection was established. The voltammetric currents of Cd²⁺ were in linear range with the target ssDNA concentration from 5.0 × 10^− 13 to 1.0 × 10^− 10 mol/L and the detection limit was estimated to be 8.9 × 10^− 14 mol/L (3σ). The proposed method showed a good promise for the sensitive detection of specific gene sequences with good selectivity for the discrimination of the mismatched sequences.     

The electrochemical detection of cadmium using surface-immobilized DNA

An electrochemical assay based on underpotential deposition (UPD) of metal has been utilised for the detection of Cd²⁺ using surface immobilized single-stranded DNA (ss-DNA). Since Cd²⁺ is able to undergo UPD on gold surface, this allows the opportunity to detect the amount of Cd²⁺ accumulated by immobilized ss-DNA directly via voltammetry. This is evidenced by the appearance of Cd²⁺/Cd⁰ electrochemistry at E^0′ of 92 mV (rather than E^0′ of −795 mV in bulk solution) at the ss-DNA modified gold electrode only after an exposure to Cd²⁺ solution. An association constant of 8.33 × 10⁵ M⁻¹ was determined from a Cd²⁺ calibration curve assuming a Langmuir-binding model for Cd²⁺ with surface-immobilized DNA. The high association constant is reflected in a low detectable concentration of 10 pM. The sensing layer can also be regenerated to metal-free status and can be reused up to 18 times without significant signal degradation.     

An electrochemical approach for detection of DNA methylation and assay of the methyltransferase activity

This work develops an electrochemical approach for rapid detection of the genomic DNA methylation level, assay of methyltransferase activity, and evaluation and screening of the inhibitors of methyltransferase. This method may be a help for the discovery of anticancer drugs.     

Ultrasensitive DNA detection using highly fluorescent bioconjugated nanoparticles

Sensitive DNA detection is extremely important in clinical diagnostics, gene therapy, and a variety of biomedical studies. We have developed a novel DNA bioanalysis method with a 0.8 fM (0.8 x 10-15 M) detection limit using a bioconjugated fluorescent nanoparticle-based sandwich assay. An organic dye silica nanoparticle is synthesized using a modified reverse microemulsion. The nanoparticles are highly fluorescent, extremely photostable, and easy for bioconjugation for bioanalysis. They exhibit an excellent signaling ability in the presence of trace amounts of DNA targets. With an effective surface modification, nonspecific binding and nanoparticle aggregation are minimized. In addition, the nanoparticle-based DNA bioanalysis assay can effectively discriminate one-base mismatched DNA sequences. We expect this nanoparticle-based assay to be widely useful in a number of biomedical applications where reproducible, selective, and ultrasensitive gene analysis is critical.     

DNA-conjugated polymers for self-assembled DNA chip fabrication.

We developed two DNA-conjugated polymers, one based on polyallylamine and the other on polyacrylic acid, for use in DNA chips. A 30-mer single-stranded DNA probe and thioctic acid were covalently attached to polyallylamine as sidechains. The same single-stranded DNA and 3-(pyridyldithio)propionyl hydrazide were covalently attached to polyacrylic acid as sidechains. Both DNA-conjugated polymers could be specifically immobilized onto a gold sensor substrate by a self-assembly technique. The interactions between fully matched DNA and each DNA-conjugated polymer were investigated by surface plasmon resonance. A gold surface modified with either DNA-conjugated polymer recognized fully matched DNA much better than unmatched DNA. The hybridization selectivity and efficiency of DNA-conjugated polyallylamine was optimized by adjusting the pH so as to reduce the effects of cationic polymer sidechains. The hybridization selectivity and efficiency of DNA-conjugated polymers were higher than those of a conventional immobilized thiol-based DNA. The coating of DNA-conjugated polymers reduced nonspecific adsorption of DNA by the gold substrate. DNA-conjugated polyacrylic acid was more selective toward fully matched DNA than was DNA-conjugated polyallylamine. Therefore, DNA-conjugated polymers show promise for application in novel DNA chips.     

Self-assembled DNA-conjugated polymer for novel DNA chip.

We developed DNA-conjugated polymer for DNA chip fabrication. A 30 mer probe DNA and disulfide bridges were covalently attached to the polymer side chain. The DNA-conjugated polymer can be specifically adsorbed on a gold substrate surface by a self-assembly technique. The interaction between fully matched DNA and DNA-conjugated polymer was investigated by surface plasmon resonance (SPR) technique. The DNA-conjugated polymer-modified gold surface highly recognized fully matched DNA, rather than unmatched DNA. Therefore, DNA-conjugated polymer can be used for novel DNA chip fabrication.     

Facile construction of targeted pH-responsive DNA-conjugated gold nanoparticles for synergistic photothermal-chemotherapy

Recently, stimuli-responsive DNA nanostructure-based nanodevices have been applied for cancer therapy. In this study, pH-responsive i-motif DNA was modified on gold nanoparticles (AuNPs) via a facile, time-saving freeze-thaw method and utilized to construct stimuli-responsive drug nanocarriers. When the environment pH changes from 7.4 to 5.0, the i-motif DNA would be folded into four-stranded (C-quadruplex) that could be characterized by circular dichroism, and the characteristic of acid stimulate was verified by fluorescence resonance energy transfer (FRET). To enhance specifical cellular uptake, MUC1 aptamer was employed as the targeting moiety. Doxorubicin (Dox) is an anticancer drug that can be efficiently intercalated into GC base pairs of DNA nanostructure to form drug-loaded nanovehicles (Dox@AuNP-MUC1). Additionally, owing to the excellent photothermal conversion efficiency of AuNPs, the synergistic effect between chemotherapy and PTT can be readily achieved by 808 nm near-infrared (NIR) irradiation, which exhibits specifically and efficiently anticancer efficiency. Hence, this multifunctional drug carrier shows the potential for synergistic photothermal-chemotherapy.     

An electrochemical DNA hybridization detection assay based on a silver nanoparticle label

A novel, sensitive electrochemical DNA hybridization detection assay, using silver nanoparticles as the oligonucleotide labeling tag, is described. The assay relies on the hybridization of the target DNA with the silver nanoparticle-oligonucleotide DNA probe, followed by the release of the silver metal atoms anchored on the hybrids by oxidative metal dissolution and the indirect determination of the solubilized Ag(I) ions by anodic stripping voltammetry (ASV) at a carbon fiber ultramicroelectrode. The influence of the relevant experimental variables, including the surface coverage of the target oligonucleotide, the duration of the silver dissolution steps and the parameters of the electrochemical stripping measurement of the silver(I) ions, is examined and optimized. The combination of the remarkable sensitivity of the stripping metal analysis at the microelectrode with the large number of silver(I) ions released from each DNA hybrid allows detection at levels as low as 0.5 pmol L(-1) of the target oligonucleotides.     

Nanoparticle-based electrochemical DNA detection

Nanoscale architectures of DNA-linked particle networks are attractive for electrical detection of DNA hybridization. This article reviews a variety of new nanoparticle/polynucleotide assemblies for advanced electrical detection of DNA sequences. Recent activity has led to innovative and powerful nanoparticle-based electrochemical DNA hybridization assays based on a variety of detection schemes. Such protocols rely on the use of colloidal gold tags, semiconductor quantum dot tracers, polymeric carrier (amplification) beads, or magnetic (separation) beads. Particularly useful have been protocols based on capturing of metal nanoparticle tracers followed by dissolution and anodic-stripping voltammetric measurement of the metal tag. Remarkable sensitivity is achieved by coupling particle-based amplification units and various amplification processes. The use of nanoparticle tracers for designing multi-target electrochemical coding protocols will also be documented.     

Novel luminescent nanoparticles for DNA detection

Highly luminescent LaF₃:Ce³⁺/Tb³⁺ nanocrystals were successfully prepared and surface functionalized via Layer-by-Layer technology. These as-prepared nanocrystals are highly resistant to photobleaching and pretty dispersible in aqueous solution. Due to the efficient luminescence quenching of the nanocrystals by nucleic acids, a facile fluorescence quenching method was developed for the detection of trace amount of nucleic acids. Under optimal conditions, the fluorescence intensity was proportional to the DNA concentration over the range of 0.60–25.0 μg mL^?1 for calf thymus DNA (ct-DNA) and 0.60–30.0 μg mL^?1 for herring sperm DNA (hs-DNA), respectively. The corresponding detection limit is 0.21 μg mL^?1 for ct-DNA and 0.31 μg mL^?1 for hs-DNA, respectively. The results indicated that the reported method is simple and rapid with wide linear range. Also, the recovery and relative standard deviation of this method are reasonable and satisfactory.     

Biocompatible ZnO/Au nanocomposites for ultrasensitive DNA detection using resonance Raman scattering

A novel method for identifying DNA microarrays based on ZnO/Au nanocomposites functionalized with thiol-oligonucleotide as probes is descried here. DNA labeled with ZnO/Au nanocomposites has a strong Raman signal even without silver acting as a surface-enhanced Raman scattering promoter. X-ray photoelectron spectra confirmed the formation of a three-component sandwich assay, i.e., constituted DNA and ZnO/Au nanocomposites. The resonance multiple-phonon Raman signal of the ZnO/Au nanocomposites as a spectroscopic fingerprint is used to detect a target sequence of oligonucleotide. This method exhibits extraordinary sensitivity and the detection limit is at least 1 fM.