In situ electrochemical distance tunneling spectroscopy of ds-DNA molecules

The electrical conductance of ds-DNA duplexes containing 8-14 base pairs modified at both ends with a -(CH(2))(6)-SH linker was measured in a buffered aqueous solution using electrochemically controlled distance tunneling spectroscopy. The tunneling experiment with self-complementary 5'-(GC)(n)()-3'-(CH(2))(6)-SH (n = 4-7) duplexes attached covalently to a gold STM tip and a Au(111) electrode shows a wide distribution of currents independent of the ds-DNA length. The voltage-induced horizontal orientation of ds-DNA within the junction results in decreased electrical conductance. The lower currents are also observed for ds-DNA molecules containing a single CA base mismatch.     

Electrochemical identification of artificial oligonucleotides related to bovine species. Potential for identification of species based on mismatches in the mitochondrial cytochrome C1 oxidase gene

Our studies show that electrochemical impedance spectroscopy (EIS) and scanning electrochemical microscopy (SECM) of films of ds-DNA on gold allow us to distinguish between mitochondrial DNA fragments of the cytochrome c(1) oxidase (mt-Cox1) of three related species of the subfamily 'Bovinae' (Bos taurus, Bison bison, and Bison bonasus). In EIS, a perfectly matched DNA gives rise to a considerably larger charge transfer resistance R(ct) compared to mismatched pairings. Differences in charge transfer resistance, ΔR(ct), before and after the addition of Zn(2+) ions provide an additional tool for identification. In addition, all ds-DNA films were studied by SECM and their kinetic parameters were determined. Perfectly matched ds-DNAs are readily distinguished from mismatched duplexes by their lower rate constants. Our system can be used multiple times by dehybridization and rehybridization of capture strands up to the 250 pmole level.     

Amperometric measurement of ds-DNA content using a peroxidase-modified electrode

An enzyme electrode with a chemically amplified response for methylene blue (MB) was constructed from a glassy carbon electrode and a layer containing immobilized horseradish peroxidase (HRP). MB is reduced on the electrode but regenerated through the HRP-catalyzed reaction in the presence of H(2)O(2). The electroreduction/regeneration cycle for MB resulted in an amplified electrode response. The enzyme electrode was applied to the highly sensitive measurement of ds-DNA. The current for MB decreased in association with its complexation with DNA, and the current response caused by DNA was also amplified through the recycling processes. The detection limit of ds-DNA (from salmon testes) was as low as 5 ng ml(-1).     

Scanning positional variations in single-nucleotide polymorphism of DNA: an electrochemical study

While there are a number of electrochemical methods reported that enable the detection of single nucleotide mismatches, the determination of mismatch position in a double stranded DNA remains an unsolved challenge. Using a model system, we systematically explored the electrochemical response of all possible positions of single nucleotide mismatches in a set of 25-mer DNA films. These ds-DNA sequences each with a single mismatch at one of the twenty-five positions were bound to gold surfaces through a Au-S linkage and analyzed by electrochemical impedance spectroscopy (EIS) and scanning electrochemical microscopy (SECM) in the absence and presence of Zn(2+). We expected a unique response from each mismatched sequence in order to discriminate the mismatch positions. A pattern emerges between the electrochemical signals and mismatch positions. The positions can be grouped broadly into positions that exhibit large differences between matched and mismatched DNA (around positions 5 and 9) and those that exhibit smaller differences (around positions 1, 13 and 23) in the charge transfer resistance ΔR(ct), evaluated by EIS, and the apparent rate constant k(0), evaluated by SECM. To the best of our knowledge, this is the first study evaluating the electrochemical response of a single nucleotide mismatch as a function of mismatch positions along an oligonucleotide sequence.     

采用电活性标记物N-(2-乙基-二茂铁)马来酰亚胺检测与表面固定的 一致性双链DNA特异性作用的p53蛋白质

建立了电化学检测表面固定捕获的野生型p53蛋白质的方法. 首先在金电极表面形成巯基化的单链DNA探针/己硫醇(HT)混合自组装膜, 随后巯基化的单链DNA探针与溶液中序列匹配的靶点DNA杂交, 所形成的一致性双链DNA捕获溶液中的野生型p53蛋白质. p53分子表面的半胱氨酸残基采用巯基特异性试剂N-(2-乙基-二茂铁)马来酰亚胺(Fc-Mi)进行衍生. 通过检测二茂铁的电化学信号来指示p53与一致性双链DNA之间的特异性相互作用. p53蛋白质与双链DNA的键合程度取决于双链DNA的序列. 该方法可检测的p53最低浓度为1.33 nmol•L－1.     

Imaging of DNA hybridization on microscopic polypyrrole patterns using scanning electrochemical microscopy (SECM): the HRP bio-catalyzed oxidation of 4-chloro-1-naphthol

We illustrate in this paper the successful combination of the direct and feedback mode of scanning electrochemical microscopy (SECM) for the writing of oligonucleotide patterns on thin gold films alongside the imaging of DNA hybridization. The patterning process was achieved using the direct mode of SECM, where the electrical field established between the SECM tip and the gold interface was used to drive the local deposition of micrometre sized polypyrrole spots to which a 15(mer) oligonucleotide (ODN) strand was linked covalently. Imaging of the deposited polypyrrole-ODNs was achieved by means of the feedback mode of SECM using Ru(NH(3))(6)(3+) as the mediator. The detection of the hybridization reaction of the ODN probes with their biotinylated complementary strands using SECM was possible after subsequent reactions with streptavidin and biotinylated horseradish peroxidase (HRP). The HRP-biocatalyzed oxidation of 4-chloro-1-naphthol (1) in the presence of H(2)O(2), and the precipitation of the insoluble product 4-chloro-1-naphthon (2) on the hybridized areas on the gold film caused a local alteration of conductivity. Such a change in conductivity was sensitively detected by the SECM tip and allowed imaging of DNA arrays in a fast and straightforward way.     

The detection of DNA deamination by electrocatalysis at DNA-modified electrodes

The method of electrocatalysis based on using a methylene blue (MB) as an electrochemical indicator and ferricyanide ions [Fe(CN)6]3- as an electron acceptor was applied in screening DNA for lesions caused by deamination of nucleobases. The damaged DNA was modeled by short 18-mer oligonucleotides containing the different number of mismatched target bases (uracil instead of cytosine residues). The hybridization capacity of these oligomers with complementary probes (immobilized on gold electrodes or free) was investigated by both electrochemical methods and UV spectroscopy. We have shown that the amplitude of the reduction signal corresponding to ferricyanide ions considerably increases in the presence of MB. This electrocatalytic effect allowed us to detect the changes in electrochemical properties of DNA caused by dU.dG mismatches. Using differential pulse voltammetry and cyclic voltammetry, we showed that the electron transport from the electrode through the double-stranded DNA to MB and then to ferricyanide ions is suppressed by the mismatches in duplex structure. According to UV-monitored melting data, single or multiple wobble dU.dG base pairs destabilize 18-mer DNA duplex by 9-27 degrees C.     

A new peptide nucleotide acid biosensor for electrochemical detection of single nucleotide polymorphism in duplex DNA via triplex structure formation

In this paper, we report a new PNA biosensor for electrochemical detection of point mutation or single nucleotide polymorphism (SNP) in p53 gene corresponding oligonucleotide based on PNA/ds-DNA triplex formation following hybridization of PNA probe with double-stranded DNA (ds-DNA) sample without denaturing the ds-DNA into single-stranded DNA (ss-DNA). As p53 gene is mutated in many human tumors, this research is useful for cancer therapy and genomic study. In this approach, methylene blue (MB) is used for electrochemical signal generation and the interaction between MB and oligonucleotides is studied by differential pulse voltammety (DPV). Probe-modified electrode is prepared by self-assembled monolayer (SAM) formation of thiolated PNA molecules on the surface of Au electrode. A significant increase in the reduction signal of MB following hybridization of the probe with the complementary double-stranded oligonucleotide (ds-oligonucleotide) confirms the function of the biosensor. The selectivity of the PNA sensor is investigated by non-complementary ds-oligonucleotides and the results support the ability of the sensor to detect single-base mismatch directly on ds-oligonucleotide. The influence of probe and ds-DNA concentrations on the effective discrimination against complementary sequence and point mutation is studied and the concentration of 10^?6 M is selected as appropriate concentration. Diagnostic performance of the biosensor is described and the detection limit is found to be 4.15 × 10^?12 M.     

Direct detection and discrimination of double-stranded oligonucleotide corresponding to hepatitis C virus genotype 3a using an electrochemical DNA biosensor based on peptide nucleic acid and double-stranded DNA hybridization

Development of an electrochemical DNA biosensor for the direct detection and discrimination of double-stranded oligonucleotide (dsDNA) corresponding to hepatitis C virus genotype 3a, without its denaturation, using a gold electrode is described. The electrochemical DNA sensor relies on the modification of the gold electrode with 6-mercapto-1-hexanol and a self-assembled monolayer of 14-mer peptide nucleic acid probe, related to the hepatitis C virus genotype 3a core/E1 region. The increase of differential pulse voltammetric responses of methylene blue, upon hybridization of the self-assembled probe with the target ds-DNA to form a triplex is the principle behind the detection and discrimination. Some hybridization experiments with non-complementary oligonucleotides were carried out to assess whether the developed DNA sensor responds selectively to the ds-DNA target. Diagnostic performance of the biosensor is described and the detection limit was found to be 1.8 × 10⁻¹² M in phosphate buffer solution, pH 7.0. The relative standard deviation of measurements of 100 pM of target ds-DNA performed with three independent probe-modified electrodes was 3.1%, indicating a remarkable reproducibility of the detection method.     

Scanning Electrochemical Microscopy for Electrochemical Detection of Single‐base Mismatches by Tagging Ferrocenecarboxylic Acid as a Redox Probe to DNA

Scanning electrochemical microscopy (SECM) was employed for sensitive detection of single base mismatches (SBMs) in a sandwiched dsDNA. Ferrocenecarboxylic acid (Fc), covalently conjugated to the dsDNA, was oxidized to Fc⁺ via the DNA‐mediated charge transfer from the underlying gold substrate, and reduced back to Fc by SECM tip generated ferrocyanide. The electrocatalytic oxidation of SECM tip‐generated ferrocyanide was sensitive to presence, as well as the type of SBMs. Apparent standard rate constants (k⁰_app) values for different SBMs, both near the electrode surface and far from it, were evaluated by SECM. The method can detect SBMs independent of their position in dsDNA.     

Scanning electrochemical microscopy determination of organic soluble MPC electron-transfer rates

In this paper, we describe a novel method for measuring the forward heterogeneous electron-transfer rate constant (kf) through the thiol monolayer of gold monolayer protected clusters (MPCs) in solution using scanning electrochemical microscopy (SECM). Applying the equations for mixed mass-transfer and electron-transfer processes, we develop a new formula using only the diffusion coefficient and the tip radius and use it as part of a new method for evaluating SECM approach curves. This method is applied to determine the electron-transfer rates from a series of SECM approach curves for monodisperse hexanethiol MPCs and for polydisperse hexanethiol, octanethiol, decanethiol, dodecanethiol, and 2-phenyethylthiol gold MPCs. Our results show that as the alkanethiol length increases the rate of electron transfer decreases in a manner consistent with the previously proposed tunneling mechanism for the electron transfer in MPCs. However, the effective tunneling coefficient, Beta, is found to be only 0.41 A-1 for alkanethiol passivated MPCs compared to typical values of 1.1 A-1 for alkanethiols as self-assembled monolayers on two-dimensional gold substrates. Similar SECM approach curve results for Pt and Au MPCs indicate that the electron-transfer rate is dependent mostly on the composition of the thiol layer and not on differences in the core metal.     

Graphene-Gold Nanoparticle-modified Electrochemical Sensor for Detection of Kanamycin Based on Target-induced Aptamer Displacement

A highly sensitive and selective label-free electrochemical sensor was developed for the determination of kanamycin. To improve the sensitivity of the electrochemical sensor, graphene-gold nanoparticles were prepared by a one-step electrochemical coreduction process and were modified on the surface of a glassy carbon electrode. The double-stranded DNA(ds-DNA) duplex probe was immobilized onto the graphene-gold nanoparticle-modified electrode. The introduction of target kanamycin induced the displacement of aptamer from the ds-DNA duplex into the solution. Methylene blue(MB) as a redox indicator monitored the current change using differential pulse voltammetry. Under optimal conditions, the designed electrochemical aptasensor exhibited a wide linear range from 0.1 pmol/L to 10 pmol/L with a detection limit of 0.03 pmol/L for kanamycin. The experimental strategy enabled the direct analysis of milk samples, and the results showed high sensitivity and good selectivity.     

Analysis of double-stranded DNA by capillary electrophoresis using poly(ethylene oxide) in the presence of hexadecyltrimethylammonium bromide

The impact of hexadecyltrimethylammonium bromide (CTAB) on the separation of ds-DNA by capillary electrophoresis in conjunction with laser-induced fluorescence (CE-LIF) detection using poly(ethylene oxide) (PEO) solution is described. The use of CTAB for improved separation reproducibility and efficiency of DNA has not been demonstrated although it is widely used for controlling the magnitude and direction of electroosmotic flow in CE. With increasing CTAB concentration, the interactions of DNA with ethidium bromide (EtBr) and with the capillary wall decrease. For the separation of DNA fragments with the sizes ranging from several base pairs (bp) to 2,176 bp, a polymer solution consisting of 0.75% poly(ethylene oxide), 100 mM TB buffer (pH 8.0), 25 microg/mL EtBr, and 0.36 microg/mL CTAB is proper. Using the PEO solution, we separated a mixture of DNA markers V (pBR 322/HaeIII digest) and VI (pBR 328/BglI digest and pBR 328/HinfI digest) within 8 min at -375 V/cm, with the limit of detection of 2.0 ng/mL based on the peak height for the 18-bp DNA fragment. The method is highly efficient (>10(6)plate/m), repeatable (RSD of the migration times <1.5%), and sensitive. In addition, it is convenient to fill a capillary (75 microm in diameter) with such a low-viscosity PEO solution by syringe pushing.     

Photoaddition to DNA by Nonintercalated Chlorpromazine Molecules

Chlorpromazine (CPZ) forms photoadducts with DNA and photosensitizes DNA strand breaks. These reactions may be responsible for the reported photomutagenicity of CPZ and for the well-known cutaneous and ocular phototoxicity associated with this drug. We have investigated whether CPZ molecules that are intercalated between base pairs in double-stranded (ds) DNA are the absorbing species for the photoaddition reaction. Quenching of CPZ fluorescence by ds-DNA gave nonlinear Stern-Volmer plots, indicating that more than one type of complex is formed. Linear dichroism spectra of CPZ in the presence of ds-DNA showed a minimum at 345 nm, indicating that the absorption maxima of intercalation complex(es) are red-shifted compared to the absorption maximum of free CPZ at 307 nm. The sum of the absorption of all CPZ complexes with ds-DNA, obtained from dialysis experiments, was broadened and maximized at about 315 nm, indicating that complexes not involving intercalation dominate the absorption spectrum at X < 350 nm. The wavelength dependence for covalent binding of CPZ to DNA was determined by irradiating ³H-CPZ in the presence of ds-DNA at 310, 322, 334, 346, 358 and 370 nm. The resulting spectrum correlated closely with the absorption spectrum of nonintercalated CPZ rather than with the spectrum of intercalated CPZ, indicating that the latter species is not the chromophore for the photoaddition reaction.     

Ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon mediated circular strand displacement polymerization and hyperbranched rolling circle amplification

Using a cascade signal amplification strategy, an ultrasensitive electrochemical biosensor for specific detection of DNA based on molecular beacon (MB) mediated circular strand displacement polymerization (CSDP) and hyperbranched rolling circle amplification (HRCA) was proposed. The hybridization of MB probe to target DNA resulted in a conformational change of the MB and triggered the CSDP in the presence of bio-primer and Klenow fragment (KF exo⁻), leading to multiple biotin-tagged DNA duplex. Furthermore, the HRCA was implemented to product amounts of double-stranded DNA (ds-DNA) fragments using phi29 DNA polymerase via biotin-streptavidin interaction. After the product of HRCA binded numerous biotinylated detection probes, an ultrasensitive electrochemical readout by further employing the streptavidin-alkaline phosphatase. The proposed biosensor exhibited excellent detection sensitivity and specificity with a log-linear response to target DNA from 0.01 fM to 10 pM as low as 8.9 aM. The proposed method allowed DNA detection with simplicity, rapidness, low cost and high specificity, which might have the potential for application in clinical molecular diagnostics and environmental monitoring.     

Label-free fluorescent detection of DNA sequence based on interaction of brilliant green with double-stranded DNA

The dye Brilliant Green (BG) is shown to be an excellent fluorogenic probe for the detection of double-stranded DNA (ds-DNA). Typically, the detection limit of a 21-mer is as low as 6 nM ((3σ), and the method can clearly distinguish between fully complementary ds-DNA and a ds-DNA with a single mismatch. Labeling is not required, hybridization and detection occur in homogenous aqueous solution in short time, and the dye is easily accessible, commercially available, and affordable.     

Voltammetric Study of Methylene Blue at Thiol SAMs‐Modified Gold Electrodes

The voltammetric behavior of methylene blue (MB) at thiol self‐assembled monolayers modified gold electrodes (SAMs/Au) has been investigated. MB exhibited a redox peak at about ?0.35 V (vs.SCE) in alkaline solution at bare gold electrodes. When the gold electrodes were modified with thiol SAMs, the peak grew due to the accumulation of MB at SAMs. With the solution pH rising, more MB was accumulated, hence the peak height increased, which differed from that at bare gold electrodes. The electrode process at SAMs/Au featured the characteristics of adsorption and/or electrode reaction controlled. The enhancing action of glutathione monolayer (GSH SAM), 3‐mercaptopropionic acid monolayer (3MPA SAM) and other thiol SAMs was compared. Among these, GSH SAM made the MB peak increase more. At GSH SAM/Au, the peak height varied linearly with MB concentration over the range of 2 μM to 400 μM. So this can be developed for the determination of MB and studies concerned. The accumulation behavior caused by GSH SAM and native fish sperm dsDNA was compared. The interaction between DNA and MB was also discussed under this condition.     

Cyclic voltammetric detection of chemical DNA damage induced by styrene oxide in natural dsDNA layer-by-layer films using methylene blue as electroactive probe

In this work, an electrochemical sensor for detecting damage of natural double-stranded DNA (dsDNA) was constructed based on PSS/{PDDA/dsDNA}₃ layer-by-layer films, where PSS was poly(styrene sulfonate) and PDDA was poly(diallyldimethyl ammonium). When the PSS/{PDDA/dsDNA}₃ films assembled on pyrolytic graphite (PG) electrodes were immersed into methylene blue (MB) solution and loaded MB into the films, the formed PSS/{PDDA/dsDNA}₃-MB films in blank buffers at pH 7.0 showed a reversible cyclic voltammetric (CV) peak pair at −0.23 V vs. SCE for MB redox couple. In blank solutions, the MB loaded into the films was released gradually from the films, but the complete reloading of MB into the films could be realized by immersing the films into MB solution again, indicating the good reversibility of MB incorporation. However, after incubation in the solution of known genotoxic agent styrene oxide (SO), the damaged PSS/{PDDA/dsDNA}₃-MB films could not return to their original and fully-loaded state with reloading of MB, and showed smaller CV peak currents than those of intact PSS/{PDDA/dsDNA}₃-MB films. The relative peak current ratio, I_p,I/I_p,III, where I_p,I was the anodic peak current of intact DNA films in blank buffers after fully loading with MB and I_p,III was that of SO-damaged DNA films after reloading with MB, increased linearly with the incubation time with SO in the range of 5–40 min with a damage rate of 0.0099 min⁻¹. While the formation of SO adducts with dsDNA had no substantial effect on the dsDNA conformation, the steric hindrance of SO adducts with guanine or adenine blocked the intercalation of MB into the base pairs of dsDNA, resulting in the decrease of CV peak currents of loaded MB. The specific intercalation of MB into dsDNA base pairs and the sensitive electrochemical response of MB, combined with the unique feature of loading reversibility of MB in the DNA layer-by-layer films, make the difference in CV response between the intact and damaged dsDNA films become pronounced in the “loading/release/reloading” procedure. This may provide a new and general approach for constructing a biosensor for screening genetoxic chemicals in vitro.     

Electron transfer at self-assembled monolayers measured by scanning electrochemical microscopy

New approaches have been developed for measuring the rates of electron transfer (ET) across self-assembled molecular monolayers by scanning electrochemical microscopy (SECM). The developed models can be used to independently measure the rates of ET mediated by monolayer-attached redox moieties and direct ET through the film as well as the rate of a bimolecular ET reaction between the attached and dissolved redox species. By using a high concentration of redox mediator in solution, very fast heterogeneous (10(8) s(-1)) and bimolecular (10(11) mol(-1) cm(3) s(-1)) ET rate constants can be measured. The ET rate constants measured for ferrocene/alkanethiol on gold were in agreement with previously published data. The rates of bimolecular heterogeneous electron transfer between the monolayer-bound ferrocene and water-soluble redox species were measured. SECM was also used to measure the rate of ET through nonelectroactive alkanethiol molecules between substrate gold electrodes and a redox probe (Ru(NH(3))(6)(3+)) freely diffusing in the solution, yielding a tunneling decay constant, beta, of 1.0 per methylene group.     

Fabricating and imaging carbon-fiber immobilized enzyme ultramicroelectrodes with scanning electrochemical microscopy.

The scanning electrochemical microscope (SECM) is used to image the activity of enzymes immobilized on the surfaces of disk-shaped carbon-fiber electrodes. SECM was used to map the concentration of enzymatically produced hydroquinone or hydrogen peroxide at the surface of a 33-microm diameter disk-shaped carbon-fiber electrode modified by an immobilized glucose-oxidase layer. Sub-monolayer coverage of the enzyme at the electrode surface could be detected with micrometer resolution. The SECM was also employed as a surface modification tool to produce microscopic regions of enzyme activity by using a variety of methods. One method is a gold-masking process in which microscopic gold patterns act as mask for producing patterns of chemical modification. The gold masks allow operation in both a positive or negative process for patterning enzyme activity. A second method uses the direct mode of the SECM to produce covalently attached amine groups on the carbon surface. The amine groups are anchors for attachment of glucose oxidase by use of a biotin/avidin process. The effect of non-uniform enzyme activity was investigated by using the SECM tip to temporarily damage an immobilized enzyme surface. SECM imaging can observe the spatial extent and time-course of the enzyme recovery process.