Alkaline phosphatase enzymatic signal amplification for fast, sensitive impedimetric DNA detection.

Enzymatic signal amplification by the deposition of insoluble product on the electrode surface enhances impedimetric DNA detection sensitivity. This work demonstrates a method which gives the required detection sensitivity at significantly reduced enzyme reaction times, and demonstrates the capability for DNA SNP discrimination of biologically relevant sequences. This opens up the prospect of more rapid and relevant multiparameter impedimetric bioassays.

Fast DNA and protein microarray tests for the diagnosis of hepatitis C virus infection on a single platform.

Hepatitis C virus (HCV) is a major cause of chronic liver disease and liver cancer, and remains a large health care burden to the world. In this study we developed a DNA microarray test to detect HCV RNA and a protein microarray to detect human anti-HCV antibodies on a single platform. A main focus of this study was to evaluate possibilities to reduce the assay time, as a short time-to-result (TTR) is a prerequisite for a point-of-care test. Significantly reducing hybridisation and washing times did not impair the assay performance. This was confirmed first using artificial targets and subsequently using clinical samples from an HCV seroconversion panel derived from a HCV-infected patient. We were able to reduce the time required for the detection of human anti-HCV antibodies to only 14 min, achieving nanomolar sensitivity. The protein microarray exhibited an analytical sensitivity comparable to that of commercial systems. Similar results were obtained with the DNA microarray using a universal probe which covered all different HCV genotypes. It was possible to reduce the assay time after PCR from 150 min to 16 min without any loss of sensitivity. Taken together, these results constitute a significant step forward in the design of rapid, microarray-based diagnostics for human infectious disease, and show that the protein microarray is currently the most favourable candidate to fill this role.

Fluorescence lifetime imaging of quantum dot labeled DNA microarrays.

Quantum dot (QD) labeling combined with fluorescence lifetime imaging microscopy is proposed as a powerful transduction technique for the detection of DNA hybridization events. Fluorescence lifetime analysis of DNA microarray spots of hybridized QD labeled target indicated a characteristic lifetime value of 18.8 ns, compared to 13.3 ns obtained for spots of free QD solution, revealing that QD labels are sensitive to the spot microenvironment. Additionally, time gated detection was shown to improve the microarray image contrast ratio by 1.8, achieving femtomolar target sensitivity. Finally, lifetime multiplexing based on Qdot525 and Alexa430 was demonstrated using a single excitation-detection readout channel.

Impedimetric detection of single-stranded PCR products derived from methicillin resistant Staphylococcus aureus (MRSA) isolates.

Using electrochemical impedance spectroscopy (EIS) the sensitive and specific detection of the antibiotic resistance gene mecA has been demonstrated. The gene sequence was obtained from clinical Staphylococcus aureus isolates. Initially a mecA specific probe was selected from hybridisation tests with a 3' and 5' version of a previously published probe sequence. When immobilised on a gold electrode in PNA form it was possible to detect hybridisation of mecA PCR product electrochemically at concentrations as low as 10nM. By incorporating an undecane-thiol and 1.8 nm glycol spacer into the PNA probe it was possible to extend the limit of detection for mecA to 10 pM. Most published studies on EIS and nucleic acid detection report the use of short artificial DNA sequences or novel signal amplification schemes which improve sensitivity whereas this study reports the successful detection of long DNA fragments produced by PCR following extraction from clinical isolates. Finally, using screen printed electrodes the paper demonstrates hybridisation monitoring of mecA in an "on-line" assay format under ambient conditions which paves the way for rapid mecA detection in point of care scenarios.

Development of immunosensors for direct detection of three wound infection biomarkers at point of care using electrochemical impedance spectroscopy.

A method for label-free, electrochemical impedance immunosensing for the detection and quantification of three infection biomarkers in both buffer and directly in the defined model matrix of mock wound fluid is demonstrated. Triggering Receptor-1 Expressed on Myeloid cells (TREM-1) and Matrix MetalloPeptidase 9 (MMP-9) are detected via direct assay and N-3-oxo-dodecanoyl-l-HomoSerineLactone (HSL), relevant in bacterial quorum sensing, is detected using a competition assay. Detection is performed with gold screen-printed electrodes modified with a specific thiolated antibody. Detection is achieved in less than 1h straight from mock wound fluid without any extensive sample preparation steps. The limits of detection of 3.3 pM for TREM-1, 1.1 nM for MMP-9 and 1.4 nM for HSL are either near or below the threshold required to indicate infection. A relatively large dynamic range for sensor response is also found, consistent with interaction between neighbouring antibody-antigen complexes in the close-packed surface layer. Together, these three novel electrochemical immunosensors demonstrate viable multi-parameter sensing with the required sensitivity for rapid wound infection detection directly from a clinically relevant specimen.

Dielectrophoretic manipulation of ribosomal RNA.

The manipulation of ribosomal RNA (rRNA) extracted from E. coli cells by dielectrophoresis (DEP) has been demonstrated over the range of 3 kHz-50 MHz using interdigitated microelectrodes. Quantitative measurement using total internal reflection fluorescence microscopy of the time dependent collection indicated a positive DEP response characterized by a plateau between 3 kHz and 1 MHz followed by a decrease in response at higher frequencies. Negative DEP was observed above 9 MHz. The positive DEP response below 1 MHz is described by the Clausius-Mossotti model and corresponds to an induced dipole moment of 3300 D with a polarizability of 7.8×10(-32) F m(2). The negative DEP response above 9 MHz indicates that the rRNA molecules exhibit a net moment of -250 D, to give an effective permittivity value of 78.5 ε(0), close to that of the aqueous suspending medium, and a relatively small surface conductance value of ∼0.1 nS. This suggests that our rRNA samples have a fairly open structure accessible to the surrounding water molecules, with counterions strongly bound to the charged phosphate groups in the rRNA backbone. These results are the first demonstration of DEP for fast capture and release of rRNA units, opening new opportunities for rRNA-based biosensing devices.

Peptide-tags for enhanced DNA microarray performance.

DNA microarrays are powerful tools for gene expression analysis and genotyping studies in research and diagnostic applications. A high sensitivity and short time-to-result are prerequisites for their practical application in the clinic. The hybridization efficiency of DNA microarrays depends on the probe density and the probe orientation and thus their accessibility for target molecules. In order to find an optimal probe immobilization procedure a set of different oligonucleotide modifications was tested on epoxy silane functionalized glass slides. It was found that histidine-tagged oligonucleotides resulted in the highest amount of bound probe and by far the best hybridization efficiencies. The detection limit obtained with histidine-tagged probes was up to two orders of magnitude lower compared to commonly used probe modifications. In order to further investigate the binding mechanism of histidine-tags towards functionalized glass substrates a set of different peptide-tags with and without free terminal amino-groups and with different amino acid compositions was tested. The results indicate an impact of the terminal amino group on the covalent surface binding and of aromatic amino acid residues on the enhanced hybridisation efficiency.

Multi-factorial analysis of class prediction error: estimating optimal number of biomarkers for various classification rules.

Machine learning and statistical model based classifiers have increasingly been used with more complex and high dimensional biological data obtained from high-throughput technologies. Understanding the impact of various factors associated with large and complex microarray datasets on the predictive performance of classifiers is computationally intensive, under investigated, yet vital in determining the optimal number of biomarkers for various classification purposes aimed towards improved detection, diagnosis, and therapeutic monitoring of diseases. We investigate the impact of microarray based data characteristics on the predictive performance for various classification rules using simulation studies. Our investigation using Random Forest, Support Vector Machines, Linear Discriminant Analysis and k-Nearest Neighbour shows that the predictive performance of classifiers is strongly influenced by training set size, biological and technical variability, replication, fold change and correlation between biomarkers. Optimal number of biomarkers for a classification problem should therefore be estimated taking account of the impact of all these factors. A database of average generalization errors is built for various combinations of these factors. The database of generalization errors can be used for estimating the optimal number of biomarkers for given levels of predictive accuracy as a function of these factors. Examples show that curves from actual biological data resemble that of simulated data with corresponding levels of data characteristics. An R package optBiomarker implementing the method is freely available for academic use from the Comprehensive R Archive Network (http://www.cran.r-project.org/web/packages/optBiomarker/).

Effect of the insulating shield thickness on the steady-state diffusion-limiting current of sphere cap microelectrodes.

The effect of the insulating shield thickness on the steady-state diffusion-limiting current of sphere cap microelectrodes is investigated. Theoretical steady-state limiting currents are obtained by using a simulation procedure, which relies on the explicit finite difference method with a fixed time grid and an exponentially spatial grid. The results obtained indicate that the current increases by decreasing the thickness of the insulating sheath or by increasing the aspect ratio of the sphere cap (h/a, where h is the height of the sphere cap and a is the electrode basal radius), similarly to other types of microelectrodes with different electrode geometry, such as disks and finite cones. The simulated data are fitted to approximate analytical expressions to describe the dependence of the limiting current on both h/a and RG (RG=b/a, where b is the overall tip radius) parameter. Theoretical currents are also compared with experimental data, which are obtained with a range of mercury-coated platinum microelectrodes having different RG and h/a values. The measurements are performed by using cyclic voltammetry at 1 mVs(-1), in aqueous solutions containing Ru(NH3)6-Cl3 as electroactive species. A good agreement (within 3%) between theoretical and experimental steady-state currents is found. Finally, SECM operating in the feedback mode is used to assess the validity of the shape parameters found by voltammetry for sphere cap microelectrodes, whose insulating shields are of a thickness comparable to the electrode radius.

Application of thin-shielded mercury microelectrodes in anodic stripping voltammetry.

The performance in anodic stripping voltammetry (ASV) of hemispherical mercury microelectrodes, fabricated by electrodeposition of liquid mercury on the surface of Pt microdisks which were surrounded by a rather thick or thin insulating shield, was compared. The Pt microdisks were produced by sealing a wire of 25 microm diameter into a glass capillary, and by coating the cylindrical length of the Pt wire with a cathodic electrophoretic paint. The ratio of the overall tip radius b, to the basal radius of the electrode a, so-called RG=b/a, was equal to 110+/-10 and 1.52+/-0.01 for the thick- and thin-shielded microdisk, respectively. The mercury microelectrodes were characterized by cyclic voltammetry at 1 mVs(-1), in 1mM Ru(NH(3))(6)(3+) aqueous solution. The steady-state voltammogram recorded with the thin-shielded mercury microelectrode displayed less hysteresis, while the steady-state current was about 30% higher than that of the thicker one. This was a consequence of the additional flux due to diffusion from behind the plane of the electrode. The flux enhancement, which was operative at the thin-shielded mercury microelectrode during the deposition step in the ASV experiments, allowed recording stripping peaks for Cd and Pb, which resulted about 32% larger than those recorded at the thicker shielded mercury microelectrode, under same experimental conditions. The usefulness of the thin-shielded mercury microelectrode for ASV measurements in real samples was verified by determining the content of heavy metal ions released in the pore water (pH 4.5) of a soil slurry.

Measurement of apparent diffusion coefficients within ultrathin nafion Langmuir-Schaefer films: comparison of a novel scanning electrochemical microscopy approach with cyclic voltammetry.

The use of scanning electrochemical microscopy (SECM) to evaluate the apparent diffusion coefficient, Dapp, of redox-active species in ultrathin Nafion films is described. In this technique, an ultramicroelectrode (UME) tip, positioned close to a film on a macroscopic electrode, is used to oxidize (or reduce) a species in bulk solution, causing the tip-generated oxidant (reductant) to diffuse to the film/solution interface. The oxidation (reduction) of film-confined species regenerates the reductant (oxidant) in solution, leading to feedback to the UME. A numerical model is developed that allows Dapp to be determined. For these studies, ultrathin films of Nafion were prepared using the Langmuir-Schaefer (LS) technique and loaded with an electroactive species, either the ferrocene derivative ferrocenyltrimethylammonium cation, FA+, or tris(2,2'-bipyridyl)ruthenium(II), Ru(bpy)32+. The morphology and the thickness of the Nafion LS films (1.5 +/- 0.2 nm per layer deposited) were evaluated using atomic force microscopy (AFM). For comparison with the SECM measurements, cyclic voltammetry (CV) was employed to evaluate the concentration of electroactive species within the Nafion LS films and to determine Dapp. The latter was found to be essentially invariant with film thickness, but the value for Ru(bpy)32+ was 1 order of magnitude larger than for FA+. CV and SECM measurements yield different values of Dapp, and the underlying reasons are discussed. In general, the Dapp values for these films are considerably smaller than for recast Nafion films, which can be attributed to the compactness of Nafion LS films. Nonetheless, the ultrathin nature of the films leads to fast response times, and we thus expect that these modified electrodes could find applications in sensing, electroanalysis, and electrocatalysis.

Fluorescence confocal laser scanning microscopy as a probe of pH gradients in electrode reactions and surface activity.

The application of fluorescence confocal laser scanning microscopy (CLSM) to quantify three-dimensional pH gradients near electrode surfaces is described. The methodology utilizes a trace quantity of a fluorescent dye, fluorescein, in solution, which fluoresces strongly above pH 6.5, to map the pH adjacent to various ultramicroelectrodes undergoing electrochemical processes that lead to pH changes. The experimental fluorescence profiles, determined by CLSM, have been compared to models by solving the underlying mass transport equations, including the effect of natural convection, using the finite element method. The methodology has been validated through studies of the galvanostatic reduction of water at both disk and ring ultramicroelectrodes. The fluorescence profiles were found to be highly sensitive to both the initial bulk solution pH and applied current in a predictable fashion. The potentiostatic reduction of oxygen has been investigated at 25- and 10-microm-diameter platinum electrodes to confirm the effective number of electrons transferred in the reaction. Finally, the application of this methodology to observe defects in microelectrode arrays, particularly those that cannot be seen by optical microscopy, is described.

Voltammetric determination of the geometrical parameters of inlaid microdisks with shields of thickness comparable to the electrode radius.

The cyclic voltammetric behavior of disk microelectrodes surrounded by thin insulating shields (TSM) was investigated from both theoretical and experimental points of view. In particular, microdisks with shields of thickness (b - a), a few electrode radii (a) were considered. A finite difference simulation procedure with a nonuniform, expanding spatial grid, already available in the literature, was employed for predicting shape and height of the voltammograms. The parameters of this numerical simulation were optimized again, and the steady-state limiting currents found in this work for a range of TSMs compared well with previous publications. The steady-state limiting current at TSMs was enhanced with respect to microelectrodes surrounded by thick insulating sheaths (i.e., b >> a), and steady-state conditions were achieved faster. Under these conditions, the difference in potential observed on the forward and backward waves, when the current is half of its maximum value (deltaE(1/2)), was almost equal to zero. Nonsteady-state cyclic voltammograms were also simulated using the optimized parameters, and the effect of scan rate on deltaE(1/2) was examined in detail. Based on this dependence, a voltammetric procedure for the simultaneous determination of microdisk radius and its insulator thickness was proposed. Experimental measurements were performed by using platinum wires, 10-12.5-microm radius, and carbon fibers, 4-microm radius, coated with 4-6-microm-thick electrophoretic paint. The shield thickness produced around the wires was such that b/a < 3. The experimental results obtained were in general congruent with the theory and demonstrated the validity of the method proposed here for the simultaneous determination of radius and shield thickness of a TSM.