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.     

Effect of monovalent cations (Li+, Na+, K+, Cs+) on self-assembly of thiol-modified double-stranded and single-stranded DNA on gold electrode

In this article we investigate the effect of monovalent cations (Li(+), Na(+), K(+), Cs(+)) on self-assembly of thiol-modified double-stranded DNA (ds-DNA) and single-stranded DNA (ss-DNA) on gold electrodes. Electrochemical characteristics (surface coverage, ion penetration and charge transfer) of ds-DNA and ss-DNA self-assembled monolayers (SAMs) formed with different monovalent cations are inspected based on six important interfacial parameters including surface coverage (Γ(m)), interfacial capacitance (C), phase angle (Φ(1 Hz)), ion transfer resistance (R(it)*), current density difference (Δj) and charge transfer resistance (R(ct)) from chronocoulometry (CC), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Three sections are included: (1) Investigation of the relationships of parameters (Γ(m), C, Φ(1 Hz), R(it)*, Δj and R(ct)) for ds-DNA-SAMs and ss-DNA-SAMs with cation types and concentrations; (2) confirmation and explanation of our experimental results combined with our recently proposed simple DNA model and literature reports; (3) exploration of the mechanism for the orders of monovalent cations (Li(+), Na(+), K(+), Cs(+)) on availing the adsorption of ds-DNA and ss-DNA molecules on gold based on their physicochemical parameters (ion size, solvation free energy and enthalpy, ion-water bond length and water exchange rate) and possible binding modes with DNA molecules. This work might provide a useful reference for understanding interactional mechanism of cations with DNA molecules.     

Scanning electrochemical microscopy imaging of DNA microarrays using methylene blue as a redox-active intercalator

Scanning electrochemical microscopy (SECM) has been employed in the imaging of DNA microarrays fabricated on gold substrates using methylene blue (MB) as a redox-active intercalator and ferrocyanide as the SECM mediator in solution. MB intercalated between base pairs of immobilized ds-DNA is electrochemically reduced via electron transfer from the underlying gold substrate, and the product is reoxidized in solution by SECM tip-generated ferricyanide. The resulting feedback current allows a heterogeneous electron-transfer rate constant for the MB-intercalated DNA to be deduced. Moreover, DNA microarray spots can be imaged at a detection level of 14 fmol/spot for ds-DNA consisting of 15 base pairs. Microarrays prepared using 20 microM DNA solutions are easily visualized, and the feasibility of detecting base pair mismatches is also demonstrated.     

Electrochemical studies on the permeable characteristics of thiol-modified double-stranded DNA self-assembled monolayers on gold

In this article we studied the permeable characteristics of thiol-modified double-stranded DNA (ds-DNA) self-assembled monolayers (SAMs) on a gold substrate assembled under different NaCl concentrations by electrochemical methods. It was based on the inspection of five important parameters including interfacial capacitance (C), phase angle (Φ(1?Hz)), ions transfer resistance (R(it)*), current density difference (Δj) and electron transfer rate (k(et)) through cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Three sections were included: (1) Investigation of the relationships of C, Φ(1?Hz), R(it)*, Δj and k(et) with NaCl concentrations and comparison with the reports from literature. Experimental results showed that ds-DNA-SAMs were permeable films. (2) Construction of a simple model for exploring the permeable characteristics of ds-DNA-SAMs on gold. (3) Confirmation of the simple model by chronocoulometry (CC) and application of the model to explain the permeable mechanism. This study was significant for exploring the mechanism of electron transfer through the interior of ds-DNA duplex helix.     

A novel protein analytical method based on hybrid-aptamer and DNA-arrayed electrodes

A novel protein assay method based on a DNA array was developed, in which human immunoglobulin E (hIgE) and its DNA aptamer were used as an analytical model. The target protein hIgE was captured by the aptamer in homogeneous solution and then the resulting hIgE-aptamer complex was hybridized onto probes self-assembled on the DNA array. Measured by electrochemical impedance spectroscopy (EIS), the charge transfer resistance (Rct) of electrodes before and after hybridization was compared. To test the selectivity of the method, four different probes with one to three mismatched bases were immobilized on respective electrodes. The results showed that the complex could be hybridized and detected out on the electrodes modified with the fully complementary sequences. In addition, the DNA array could be employed to analyze multiple samples selectively with the matched aptamer.     

Y-type, C-rich DNA probe for electrochemical detection of silver ion and cysteine

An electrochemical assay for the detection of silver ion was reported, which was based on the interaction of the Y-type, C-rich ds-DNA with Ag(+). Upon addition of Ag(+), Y-type, C-rich ds-DNA could form an intramolecular duplex, in which Ag(+) can selectively bind to cytosine-cytosine (C-C) mismatches forming C-Ag(+)-C complex. The binding result was evaluated by electrochemical impedance spectroscopy (EIS) and analyzed with the help of Randles' equivalent circuits. The differences of charge transfer resistance, ΔR(CT), after and before the addition of Ag(+), allows the detection and quantitative analysis of Ag(+) with a detection limit of 10 fM. Moreover, cysteine (Cys) was applied to remove Ag(+) from the C-Ag(+)-C complex, which allowed the Ag(+) sensor to be reproduced. In the same way, ΔR(CT) for the C-Ag(+)-C system in the absence and presence of Cys allows the detection of Cys at a concentration as low as 100 fM. Finally, the potential application of the Ag(+) sensor was also explored, such as in lake and drinking water.     

Preparation and characterization of polystyrene/Ag core-shell microspheres--a bio-inspired poly(dopamine) approach

In this work, we have systematically investigated the formation and characterization of Self-assembled Monolayer (SAM) films of several silanes on indium tin oxide (ITO) surfaces. Silane molecules having different domains namely substrate binding domain (siloxanes), electron transport region (aliphatic and aromatic spacer) and terminal functional groups (-SH, -CH(3) groups) are employed for the study in order to tune the electron transfer (ET) behaviour across SAM modified electrode-electrolyte interface. Structural characterization of these monolayer films is carried out using X-ray photoelectron spectroscopy (XPS) studies. Wettability (hydrophilic and hydrophobic nature) of such modified electrodes is evaluated using contact angle measurements. ET behaviour of these modified electrodes is investigated by electrochemical techniques namely cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) using K(4)Fe(II)(CN)(6)|K(3)Fe(III)(CN)(6) redox couple as a probe. Disappearance of redox peaks in the CV measurements and formation of semicircle having a higher charge transfer resistance (R(ct)) values during EIS studies suggest that the resultant monolayer films are compact, highly ordered with very low defects and posses good blocking property with less pinholes. The heterogeneous ET rate constant (k) values are determined from EIS by fitting them to an appropriate equivalent circuit model. Based on our results, we comment on tuning the ET behaviour across the interface by a proper choice of spacer region.     

Towards the electrochemical identification of species

Different properties of surface grafted ds-DNA films resulting from the presence of base-pair mismatches provide the basis for an electrochemical method for the identification of species.     

Investigation of Active and Inactivated Yeast Cells by Scanning Electrochemical Impedance Microscopy

Scanning electrochemical microscopy (SECM), electrochemical impedance spectroscopy (EIS) and scanning electrochemical impedance microscopy (SEIM) were used to investigate electrochemical activity of active and inactivated yeast Saccharomyces cerevisiae cells. SEIM experiment was performed using a unique electrochemical impedance spectrometer with a fast Fourier transform (FFT‐EIS) function, which enabled simultaneously perturb/evaluate electrochemical system at 50 frequencies. This allowed very quick observing the differences between impedance spectra, which were taken every few seconds. Therefore, we were able to apply SEIM for relatively fast determination of electrochemical impedance dependence on the distance between ultramicroelectrode (UME) and surface modified by immobilized yeast cells. It was determined that electrochemical activity and ‘breathing’ (a consumption of dissolved oxygen) of yeast can be electrochemically observed when the distance between UME and surface of yeast cells is in the range from 0 μm to 25 μm. Therefore, 25 μm is the maximum distance suitable for efficient investigation of yeast cell activity when experiments are performed in FFT‐SEIM mode. Charge transfer resistance of active and inactivated yeast cells was determined using EIS. It was calculated that charge transfer resistance of active yeast cells is 1.5 times lower than that of inactivated yeast cells. Lipophilic vitamin K₃ (Vit‐K₃) and hydrophilic vitamin K₁ (Vit‐K₁) were mixtured and used as redox mediators for charge transfer from yeast cells.     

A novel method for glucose determination based on electrochemical impedance spectroscopy using glucose oxidase self-assembled biosensor

A method is developed for quantitative determination of glucose using electrochemical impedance spectroscopy (EIS). The method is based on immobilized glucose oxidase (GOx) on the topside of gold mercaptopropionic acid self-assembled monolayers (Au-MPA-GOx SAMs) electrode and mediation of electron transfer by parabenzoquinone (PBQ). The PBQ is reduced to hydroquinone (H(2)Q), which in turn is oxidized at Au electrode in diffusion layer. An increase in the glucose concentration results in an increase in the diffusion current density of the H(2)Q oxidation, which corresponds to a decrease in the faradaic charge transfer resistance (R(ct)) obtained from the EIS measurements. Glucose is quantified from linear variation of the sensor response (1/R(ct)) as a function of glucose concentration in solution. The method is straightforward and nondestructive. The dynamic range for determination of glucose is extended to more than two orders of magnitude. A detection limit of 15.6 microM with a sensitivity of 9.66 x 10(-7) Omega(-1)mM(-1) is obtained.     

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.     

Multi-wall carbon nanotubes (MWCNTs)-doped polypyrrole DNA biosensor for label-free detection of genetically modified organisms by QCM and EIS

In this paper, we describe DNA electrochemical detection for genetically modified organism (GMO) based on multi-wall carbon nanotubes (MWCNTs)-doped polypyrrole (PPy). DNA hybridization is studied by quartz crystal microbalance (QCM) and electrochemical impedance spectroscopy (EIS). An increase in DNA complementary target concentration results in a decrease in the faradic charge transfer resistance (R_ct) and signifying “signal-on” behavior of MWCNTs-PPy-DNA system. QCM and EIS data indicated that the electroanalytical MWCNTs-PPy films were highly sensitive (as low as 4 pM of target can be detected with QCM technique). In principle, this system can be suitable not only for DNA but also for protein biosensor construction.     

Electrochemical properties of interface formed by interlaced layers of DNA- and lysozyme-coated single-walled carbon nanotubes

Multifunctional coatings were produced by the layer by layer assembly of single-walled carbon nanotubes (SWNT) dispersed in DNA and lysozyme (LSZ) on an insulating glass substrate. The electrochemical properties of these mechanically robust biocoatings were characterized for the first time using scanning electrochemical microscopy (SECM) and impedance spectroscopy (IS). SECM surface analysis demonstrated an increase in tip current with a corresponding increase in the number of oppositely polarized interlaced layers, indicating that subsequent layers were not electrically insulated from each other and a direct correlation exists between SECM feedback response and the number of layers. The rate of charge transport was also dependent on the chemical composition/polarity of the outermost surface layer. Coatings terminating in SWNT-DNA resulted in more positive feedback than those terminating in SWNT-LSZ. IS analysis demonstrated that the SWNT-DNA had a low charge transfer resistance in comparison with SWNT-LSZ, which is consistent with the results obtained by SECM. These results enable enhanced fundamental understanding and prediction of the electrical properties of SWNT-biopolymer layers with controlled interlaced polarities and orientation. Furthermore, these finding highlight the potential for SWNT-biopolymers in electronic and sensing applications.     

Review: Recent applications of scanning electrochemical microscopy to the study of charge transfer kinetics

Scanning electrochemical microscopy (SECM) has been proven to be a valuable technique for the quantitative investigation and surface analysis of a wide range of processes that occur at interfaces. In particular, there is a great deal of interest in studying the kinetics of charge transfer characteristics at the solid/liquid and liquid/liquid interface. This overview outlines recent advances and applications of SECM to the investigation of charge transfer reactions at the solid/liquid interface and liquid/liquid interface.     

In situ hybridization of PNA/DNA studied label-free by electrochemical impedance spectroscopy

The in situ hybridization kinetics of label-free DNA on mixed monolayers of peptide nucleic acid (PNA) and 6-mercapto-1-hexanol (MCH) on Au electrodes was investigated by electrochemical impedance spectroscopy (EIS) and used to discriminate the fully complementary DNA from the single-base mismatched hybrids.     

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.     

Progress in Scanning Electrochemical Microscopy by Coupling with Electrochemical Impedance and Quartz Crystal Microbalance

Scanning electrochemical microscopy (SECM) is a powerful technique for performing quantitative measurements at a local scale. This paper covers the development of combinations of SECM with electrochemical impedance spectroscopy (EIS) and electrochemical quartz crystal microbalance (EQCM). Basic aspects are described and potential applications reported by several research groups are covered. The unique advantages of the coupled techniques—with additional information being obtained from each coupling—are also discussed.     

Scanning electrochemical microscopy. 51. Studies of self-assembled monolayers of DNA in the absence and presence of metal ions

Scanning electrochemical microscopy was used to examine electron transfer across a self-assembled monolayer of thiol-modified DNA duplexes on a gold electrode. The apparent rate constant for heterogeneous ET from a solution redox probe, Fe(CN)6(3-/4-), to the gold surface through ds-DNA was 4.6 (+/-0.2) x 10(-7) cm/s. With the addition of Zn2+, which resulted in the formation of a metalated DNA (M-DNA) monolayer, the rate constant increased to 5.0 (+/-0.3) x 10(-6) cm/s. Upon treating M-DNA with EDTA, the zinc ions were released from the monolayer and the original rate constant for the DNA duplexes was restored. The enhanced ET rate was also observed at a DNA monolayer treated with Ca2+ or Mg2+, which does not complex by the DNA bases to form M-DNA. The binding of these cations facilitated the monolayer penetration by the probe mediator Fe(CN)6(3-/4-) and accordingly caused an increased redox signal of the mediator at the ds-DNA-modified electrode. Cationic or neutral mediators were not blocked by the ds-DNA monolayer. These results suggest that although the increased electron transport through M-DNA could partially be ascribed to the intrinsic enhancement of electric conductivity of M-DNA, which has been confirmed by photochemical studies, the change in the surface charge of DNA monolayers on the electrode caused by the binding of metal ions to DNA molecules may play a more important role in the enhancement of current with M-DNA.     

不同浓度比的硫酸根和氯离子溶液中钝化膜的半导体特性转变机制研究

800合金作为核电站蒸汽发生器的一种关键材料,服役环境下其表面钝化膜的特性一直是人们研究的热点. 本文用Mott-Schottky方法研究了800合金在不同硫酸根离子和氯离子浓度比的溶液中钝化膜的半导体特性,并结合电化学阻抗谱（EIS）、扫描电镜（SEM）、扫描电化学显微镜（SECM）研究了钝化膜的耐蚀性和表面活性. Mott-Schottky结果表明,800合金表面钝化膜的半导体特性与溶液中硫酸根、氯离子的浓度比有关,随硫酸根与氯离子浓度比的降低,半导体特性发生转变. 当硫酸根与氯离子的浓度比较高时,钝化膜为p型半导体;而当硫酸根与氯离子的浓度比较低时,钝化膜为n型半导体. EIS、SECM、SEM结果表明,随浓度比的降低钝化膜由过钝化溶解转为明显的点蚀特征,钝化膜表面活性增加. 钝化膜特性的改变与其半导体类型的转变密切相关,而半导体特性的转变由氯离子、硫酸根离子在800合金钝化膜表面的竞争吸附所致,其在表面的竞争吸附直接影响钝化膜表面发生的化学反应,改变电极/溶液界面电势差,使钝化膜中的空位类型改变,最终决定半导体类型.     

Deposition of polyaniline on RVC electrodes: effect of substrate thickness

Polyaniline films, obtained by either chemical or electrochemical deposition on reticulated vitreous carbon (RVC), were investigated as a function of the substrate thickness. The electrochemical properties of these RVC/Pani electrodes were assessed by cyclic voltammetry and electrochemical impedance spectroscopy (EIS), whereas the morphology of the Pani films on RVC was analyzed by scanning electron microscopy (SEM). The cyclic voltammetric results revealed that the oxidation/reduction charges for electrodeposited polyaniline decrease as the RVC thickness is increased. Conversely, the charge densities for the chemically deposited films do not present a significant dependence on the substrate thickness. Two time constants, appearing in all the EIS spectra, indicate that an ohmic drop effect within the RVC substrate affects the polymer electrodeposition and the electrochemical behavior of the obtained electrodes. Therefore, an electric equivalent circuit considering the different electrochemical environments at the outer and inner RVC surfaces was proposed to analyze the EIS data.