Automated detection and quantitation of bacterial RNA by using electrical microarrays

Low-density electrical 16S rRNA specific oligonucleotide microarrays and an automated analysis system have been developed for the identification and quantitation of pathogens. The pathogens are Escherichia coli, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus epidermidis, which are typically involved in urinary tract infections. Interdigitated gold array electrodes (IDA-electrodes), which have structures in the nanometer range, have been used for very sensitive analysis. Thiol-modified oligonucleotides are immobilized on the gold IDA as capture probes. They mediate the specific recognition of the target 16S rRNA by hybridization. Additionally three unlabeled oligonucleotides are hybridized in close proximity to the capturing site. They are supporting molecules, because they improve the RNA hybridization at the capturing site. A biotin labeled detector oligonucleotide is also allowed to hybridize to the captured RNA sequence. The biotin labels enable the binding of avidin alkaline phophatase conjugates. The phosphatase liberates the electrochemical mediator p-aminophenol from its electrically inactive phosphate derivative. The electrical signals were generated by amperometric redox cycling and detected by a unique multipotentiostat. The read out signals of the microarray are position specific current and change over time in proportion to the analyte concentration. If two additional biotins are introduced into the affinity binding complex via the supporting oligonucleotides, the sensitivity of the assays increase more than 60%. The limit of detection of Escherichia coli total RNA has been determined to be 0.5 ng/microL. The control of fluidics for variable assay formats as well as the multichannel electrical read out and data handling have all been fully automated. The fast and easy procedure does not require any amplification of the targeted nucleic acids by PCR.     

Impedance sensing of DNA binding drugs using gold substrates modified with gold nanoparticles

Interfacial interactions between immobilized DNA probes and DNA-specific sequence binding drugs were investigated using impedance spectroscopy toward the development of a novel biosensing scheme. The impedance measurements are based on the charge-transfer kinetics of the [Fe(CN)6]3-/4- redox couple. Compared to bare gold surfaces, the immobilization of DNA and then the DNA-drug interaction on electrode surfaces altered the capacitance and the interfacial electron resistance and thus diminished the charge-transfer kinetics by reducing the active area of the electrode or by preventing the redox species from approaching the electrode. Electrochemical deposition of gold nanoparticles on a gold electrode surface showed significant improvement in sensitivity. DNA-capped gold nanoparticles on electrodes act as selective sensing interfaces with tunable sensitivity due to higher amounts of DNA probes and the concentric orientation of the DNA self-assembled monolayer. The specificity of the interactions of two classical minor groove binders, mythramycin, a G-C specific-DNA binding anticancer drug, netropsin, an A-T specific-DNA binding drug and an intercalator, nogalamycin on AT-rich DNA-modified substrate and GC-rich DNA-modified substrate are compared. Using gold nanoparticle-deposited substrates, impedance spectroscopy resulted in a 20-40-fold increase in the detection limit. Arrays of deposited gold nanoparticles on gold electrodes offered a convenient tool to subtly control probe immobilization to ensure suitably adsorbed DNA orientation and accessibility of other binding molecules.     

On-chip electric field driven electrochemical detection using a poly(dimethylsiloxane) microchannel with gold microband electrodes

An external electric field driven in-channel detection technique for on-chip electrochemical detection in micro fabricated devices is described based on a microfluidic system containing an array of 20 microband electrodes. It is shown that an external electric field induces a potential difference between two gold microband electrodes in a poly(dimethylsiloxane) (PDMS) microchannel, and that this enables the electrochemical detection of electroactive species such as ascorbic acid and Fe(CN) 6 (4-). The results, which are supported by simulations of the behavior of the microband electrodes in the microfluidic system, show that the induced potential difference between the electrodes can be controlled by altering the external electric field or by using different microbands in the microband array. As the obtained currents depend on the concentrations of electroactive species in the flowing solution and the detection can be carried out anywhere within the channel without interference of the external electric field, the present approach significantly facilitates electrochemical detection in capillary electrophoresis. This approach consequently holds great promise for application in inexpensive portable chip-based capillary electrophoresis (CE) devices.     

Focused ion beam production of nanoelectrode arrays

We present a method for the production of nanoelectrodes using focussed ion beam techniques (FIB). The electrodes utilise nanometric holes milled in a silicon nitride based pasivation layer, followed by wet etching of a silicon oxide based pasivation layer, to expose an underlying gold electrode. After functionalisation using a surface assembled monolayer and an electrochemically grown polypyrrole, these gold nanoelectrodes have been tested, via cyclic voltammetry, in the detection of [Fe(CN)₆]^4−/3− ions. The nanoelectrodes will be used to investigate the electrical properties of nanometric biological specimen.     

Separation high voltage field driven on-chip amperometric detection in capillary electrophoresis

A new potentiostatless detection scheme for amperometric detection in capillary electrophoresis is presented based on the use of microband array electrodes positioned in the capillary electrophoresis electric field. In the present study, the spatial potential difference in the CE separation high-voltage field was measured using two gold microband electrodes positioned in the proximity of the capillary outlet. The induced potential difference between the two electrodes was recorded as a function of the applied separation high voltage and the dependence of the electrochemically generated current on the high-voltage field, and the concentration of a redox couple (Fe(CN)6(4-)/Fe(CN)6(3-)) was investigated. The results show that plots of the generated current versus the CE separation voltage have the same shape as cyclic voltammograms obtained with the same electrodes in a traditional potentiostatic setup and that the current is proportional to the concentration of the redox couple. As a decoupling device is not needed, the described potentiostatless approach significantly simplifies the instrumental setup for amperometric detection. This approach consequently holds great promise for application in inexpensive portable chip-based CE devices.     

A monolithic silicon optoelectronic transducer as a real-time affinity biosensor

An optical real-time affinity biosensor, which is based on a monolithic silicon optoelectronic transducer and a microfluidic module, is described. The transducer monolithically integrates silicon avalanche diodes as light sources, silicon nitride optical fibers, and p/n junction detectors and efficiently intercouples these elements through a self-alignment technique. The transducer surface is hydrophilized by oxygen plasma treatment, silanized with (3-aminopropyl)triethoxysilane and bioactivated through adsorption of the biomolecular probes. The use of a microfluidic module allows real-time monitoring of the binding reaction of the gold nanoparticle-labeled analytes with the immobilized probes. Their binding within the evanescent field at the surface of the optical fiber causes attenuated total reflection of the waveguided modes and reduction of the detector photocurrent. The biotin-streptavidin model assay was used for the evaluation of the analytical potentials of the device developed. Detection limits of 3.8 and 13 pM in terms of gold nanoparticle-labeled streptavidin were achieved for continuous- and stopped-flow assay modes, respectively. The detection sensitivity was improved by silver plating of the immobilized gold nanoparticles, and a detection limit of 20 fM was obtained after 20-min of silver plating. In addition, two different analytes, streptavidin and anti-mouse IgG, were simultaneously assayed on the same chip demonstrating the multianalyte potential of the sensor developed.     

A quadruple-scanning-probe force microscope for electrical property measurements of microscopic materials

Four-terminal electrical measurement is realized on a microscopic structure in air, without a lithographic process, using a home-built quadruple-scanning-probe force microscope (QSPFM). The QSPFM has four probes whose positions are individually controlled by obtaining images of a sample in the manner of atomic force microscopy (AFM), and uses the probes as contacting electrodes for electrical measurements. A specially arranged tuning fork probe (TFP) is used as a self-detection force sensor to operate each probe in a frequency modulation AFM mode, resulting in simultaneous imaging of the same microscopic feature on an insulator using the four TFPs. Four-terminal electrical measurement is then demonstrated in air by placing each probe electrode in contact with a graphene flake exfoliated on a silicon dioxide film, and the sheet resistance of the flake is measured by the van der Pauw method. The present work shows that the QSPFM has the potential to measure the intrinsic electrical properties of a wide range of microscopic materials in situ without electrode fabrication.     

Electrochemical surface plasmon resonance measurement based on gold nanohole array fabricated by nanoimprinting technique

In this paper, we describe our development of an electrochemical surface plasmon resonance (EC-SPR) measurement device based on a bottom-filled gold nanohole array. The polymer based gold nanohole array was fabricated with a UV nanoimprint technique and electron beam gold deposition. Direct reflection mode measurement was used to monitor the SPR dip in the reflection spectra. A cyclic voltammogram was also operated by using the standard three electrodes containing working electrode having a gold nanohole array and counter and reference electrodes. The gold nanohole array was modified with an osmium-poly(vinylpyridine)-wired horseradish peroxidase (Os-gel-HRP) film, and its redox state induced by the change in potential was monitored simultaneously. The redox state of the local film was obtained simply by scanning the sample substrate stage. The substrate modified with Os-gel-HRP film was incorporated in a microfluidic chip, and then the hydrogen peroxide was determined in terms of the redox change in the Os complex mediator from the slope of the SPR dip shift. The linear relation of hydrogen peroxide from 10 to 250 μM was successfully monitored, and a high conversion efficiency was realized.     

Scanning electrochemical microscopy investigations of monolayers bound to p-type silicon substrates

p-Si type electrodes modified with different organic monolayers were investigated by reaction with radical anion and cation electrogenerated at a microelectrode operating in the configuration of a scanning electrochemical microscope. The method proves to be a convenient tool for investigating both the quality and the redox properties of the layer as previously demonstrated on metallic electrodes especially when the sample cannot be electrically connected. Approach curves recorded with the different mediators were used to investigate the electron-transfer rates across alkyl monolayers bound to p-type silicon substrates. Preliminary results indicate that the interfacial electron transfer occurs via electron tunneling through the organic layer as generally described for SAMs grafted on gold electrodes.     

A microfabricated biosensor for detecting foodborne bioterrorism agents

A biosensor for the detection of pathogenic bacteria was developed for biosecurity applications. The sensor was fabricated using photolithography and incorporates heterobifunctional crosslinkers and immobilized antibodies. The sensor detected the change in impedance caused by the presence of bacteria immobilized on interdigitated gold electrodes and was fabricated from (100) silicon with a 2-/spl mu/m layer of thermal oxide as an insulating layer. The sensor has a large active area of 9.6 mm/sup 2/ and consists of two interdigital gold electrode arrays each measuring 0.8 /spl times/ 6 mm. Pathogenic Escherichia coli and Salmonella infantis were tested in serially diluted pure culture. Analyte specific antibodies were immobilized to the oxide between the electrodes to create a biological sensing surface. After immersing the biosensor in solution, the impedance across the interdigital electrodes was measured. Bacteria cells present in the sample solution attached to the antibodies and became tethered to the electrode array thereby causing a change in measured impedance. The biosensor was able to discriminate between different cellular concentrations from 10/sup 4/ - 10/sup 7/ CFU/mL (colony-forming units per milliliter) in solution. The sample testing process, including data acquisition, required 5 min. The design, fabrication, and testing of the biosensor is discussed along with the implications of these findings toward further biosensor development.     

Design and fabrication of a microimpedance biosensor for bacterial detection

A biosensor for bacterial detection was developed based on microelectromechanical systems, heterobifunctional crosslinkers and immobilized antibodies. The sensor detected the change in impedance caused by the presence of bacteria immobilized on interdigitated gold electrodes and was fabricated from (100) silicon with a 2-/spl mu/m layer of thermal oxide as an insulating layer. The sensor active area is 9.6 mm/sup 2/ and consists of two interdigital gold electrode arrays measuring 0.8 /spl times/ 6 mm. Escherichia coli specific antibodies were immobilized to the oxide between the electrodes to create a biological sensing surface. The impedance across the interdigital electrodes was measured after immersing the biosensor in solution. Bacteria cells present in the sample solution attached to the antibodies and became tethered to the electrode array, thereby causing a change in measured impedance. The biosensor was able to discriminate between different cellular concentrations from 10/sup 5/ to 10/sup 7/ CFU/mL in pure culture. The sample testing process, including data acquisition, required 5 min. The design, fabrication, and testing of the biosensor is discussed along with the implications of these findings toward further biosensor development.     

An addressable microelectrode array for electrochemical detection

Column and row electrodes on two different glass substrates were orthogonally arranged in order to assemble an addressable microelectrode device for the purpose of comprehensive electrochemical detection. Amperometric signal at the individual crossing point of the column and row electrodes was detected separately on the basis of redox cycling of localized electroactive species occurring between the electrodes. The addressable microelectrode device was simple and could be easily assembled; however, it comprised as many as 10 x 10 addressable detection points on a single chip. The basic electrochemical performance of the device was investigated by using the ferricyanide/ferrocyanide redox couple. Electrochemical responses at 100 individual points could be collected within 22 s. The present device was successfully used for imaging the spots of alkaline phosphatase on the array substrate. The results indicate that the device can be applied to comprehensive and high-throughput detection and imaging of biochemical species.     

Effect of processable polyindole and nanostructured domain on the selective sensing of dopamine

The effect of carboxylic acid functionality present in polymer backbone is reported on electrochemical sensing of dopamine (DA). The electropolymerized conducting polymers made from carboxylic acid substituted indole at positions − 5 and − 6 are found processable in aqueous medium and are compatible with suitable additives/precursors for fabricating polymer modified electrodes (PMEs). The modified electrodes are fabricated following two methods, i.e.: (1) the processable polymers are cast over glassy carbon electrode (GCE) using Nafion® followed by chemical modification using hydrophobic organic redox mediators and (2) the processable polymers are encapsulated within organically modified silicate (Ormosil) matrix along with the hydrophilic redox mediator followed by incorporation of silver and gold nanoparticles. The electrochemical performances of these modified electrodes show selective sensing of DA with major findings: (i) both polymers introduced selectivity in electrochemical sensing of DA with analogous sensitivity, (ii) sensitivity is enhanced when hydrophobic organic redox mediators are coupled with modified electrode matrix involving Nafion®, (iii) the polymers are suitable for encapsulation within ormosil matrix thus introducing nanostructured network for further improvement in sensitivity of DA analysis, (iv) the presence of gold and silver nanoparticles within ormosil matrix along with polymers caused > 100 fold increase in sensitivity of DA sensing with lowest detection limit to the order of 100 nM.     

Epitaxial insertion of gold silicide nanodisks during the growth of silicon nanowires

Nanodisk-shaped, single-crystal gold silicide heterojunctions were inserted into silicon nanowires during vapor-liquid-solid growth using Au as a catalyst within a specific range of chlorine-to-hydrogen atomic ratio. The mechanism of nanodisk formation has been investigated by changing the source gas ratio of SiCl4 to H2. We report that an over-supply of silicon into the Au-Si liquid alloy leads to highly supersaturated solution and enhances the precipitation of Au in the silicon nanowires due to the formation of unstable phases within the liquid alloy. It is shown that the gold precipitates embedded in the silicon nanowires consisted of a metastable gold silicide. Interestingly, faceting of gold silicide was observed at the Au/Si interfaces, and silicon nanowires were epitaxially grown on the top of the nanodisk by vapor-liquid-solid growth. High resolution transmission electron microscopy confirmed that gold silicide nanodisks are epitaxially connected to the silicon nanowires in the direction of growth direction. These gold silicide nanodisks would be useful as nanosized electrical junctions for future applications in nanowire interconnections.     

High-performance taste sensor made from Langmuir-Blodgett films of conducting polymers and a ruthenium complex

A sensor array made up of nanostructured Langmuir-Blodgett (LB) films is used as an electronic tongue capable of identifying sucrose, quinine, NaCl, and HCl at the parts-per-billion (ppb) level, being in some cases 3 orders of magnitude below the human threshold. The sensing units comprise LB films from conducting polymers and a ruthenium complex transferred onto gold interdigitated electrodes. Impedance spectroscopy is used as the principle of detection, and the importance of using nanostructured films is confirmed by comparing results from LB films with those obtained from cast films.     

Characterization of Nanoporous Silicon-Based DNA Biosensor for the Detection of Salmonella Enteritidis

A biosensor for the detection of food-borne pathogens (Salmonella Enteritidis) was fabricated based on nanoporous silicon (NPS). P-type silicon wafers (100, 0.01 ) were anodized electrochemically in an electrochemical Teflon cell, containing ethanoic hydrofluoric acid solution to produce the porous layer on the silicon surface. The porous silicon surface was functionalized with DNA probes specific to the insertion element (Iel) gene of Salmonella Enteritidis. A biotin-streptavidin system was utilized to characterize the availability of the nanopores and the specificity of the DNA probe. Based on the electrical property of DNA, redox indicators and cyclic voltammetry were used for the characterization of the biosensor. Results showed that the DNA probe was specific to the target DNA, and the porous silicon-based biosensor had more active surface area and higher sensitivity (1 ng/mL) than the planar silicon-based biosensor. This simple, label-free porous silicon-based biosensor has potential applications in high-throughput detection of pathogens.     

Chip cleaning and regeneration for electrochemical sensor arrays

Sensing systems based on electrochemical detection have generated great interest because electronic readout may replace conventional optical readout in microarray. Moreover, they offer the possibility to avoid labelling for target molecules. A typical electrochemical array consists of many sensing sites. An ideal micro-fabricated sensor-chip should have the same measured values for all the equivalent sensing sites (or spots). To achieve high reliability in electrochemical measurements, high quality in functionalization of the electrodes surface is essential. Molecular probes are often immobilized by using alkanethiols onto gold electrodes. Applying effective cleaning methods on the chip is a fundamental requirement for the formation of densely-packed and stable self-assembly monolayers. However, the available well-known techniques for chip cleaning may not be so reliable. Furthermore, it could be necessary to recycle the chip for reuse. Also in this case, an effective recycling technique is required to re-obtain well cleaned sensing surfaces on the chip. This paper presents experimental results on the efficacy and efficiency of the available techniques for initial cleaning and further recycling of micro-fabricated chips. Piranha, plasma, reductive and oxidative cleaning methods were applied and the obtained results were critically compared. Some interesting results were attained by using commonly considered cleaning methodologies. This study outlines oxidative electrochemical cleaning and recycling as the more efficient cleaning procedure for electrochemical based sensor arrays.     

Laser-triggered high-voltage plasma switching with diffractive optics

High-power lasers can be used to induce ionization of gases and thereby enable rapid triggering of electrical discharge devices, potentially faster than any devices based on mechanical or solid-state switching. With diffractive optical elements (DOEs) the laser light can conveniently be directed to positions within the gas so that an electrical discharge between two high-voltage electrodes is triggered reliably and rapidly. Here we report on two different types of DOE used for creating an electrical discharge in pure argon for potential high-voltage applications. One is the diffractive equivalent of a conventional axicon that yields an extended, and continuous, high-intensity focal region between the electrodes. The other is a multiple-focal-distance kinoform-a DOE that is designed to produce a linear array of 20 discrete foci, with high peak intensities, between the electrodes. We show that DOEs enable efficient, rapid switching and may provide increased flexibility in the design of novel electrode configurations.     

Label-free electrochemical detection for aptamer-based array electrodes

An electrochemical impedance spectroscopy method of detection for aptamer-based array electrodes is reported in which the binding of aptamers immobilized on gold electrodes leads to impedance changes associated with target protein binding events. Human IgE was used as a model target protein and incubated with the aptamer-based array consisting of single-stranded DNA containing a hairpin loop. To increase the binding efficiency for proteins, a hybrid modified layer containing aptamers and cysteamine was fabricated on the photolithographic gold surface through molecular self-assembly. Atomic force microscopy analysis demonstrated that human IgE could be specifically captured by the aptamer and stand well above the self-assembled monolayer (SAM) surface. Compared to immunosensing methods using anti-human IgE antibody as the recognition element, impedance spectroscopy detection could provide higher sensitivity and better selectivity for aptamer-modified electrodes. The results of this method show good correlation for human IgE in the range of 2.5-100 nM. A detection limit of 0.1 nM (5 fmol in a 50-microL sample) was obtained, and an average of the relative standard deviation was <10%. The method herein describes the first label-free detection for arrayed electrodes utilizing electrochemical impedance spectroscopy.     

Metal nanoparticle-based electrochemical stripping potentiometric detection of DNA hybridization

A new nanoparticle-based electrical detection of DNA hybridization, based on electrochemical stripping detection of the colloidal gold tag, is described. In this protocol, the hybridization of a target oligonucleotide to magnetic bead-linked oligonucleotide probes is followed by binding of the streptavidin-coated metal nanoparticles to the captured DNA, dissolution of the nanometer-sized gold tag, and potentiometric stripping measurements of the dissolved metal tag at single-use thick-film carbon electrodes. An advanced magnetic processing technique is used to isolate the DNA duplex and to provide low-volume mixing. The influence of relevant experimental variables, including the amounts of the gold nanoparticles and the magnetic beads, the duration of the hybridization and gold dissolution steps, and the parameters of the potentiometric stripping operation upon the hybridization signal, is examined and optimized. Transmission electron microscopy micrographs indicate that the hybridization event leads to the bridging of the gold nanoparticles to the magnetic beads. Further signal amplification, and lowering of the detection limits to the nanomolar and picomolar domains, are achieved by precipitating gold or silver, respectively, onto the colloidal gold label. The new electrochemical stripping metallogenomagnetic protocol couples the inherent signal amplification of stripping metal analysis with discrimination against nonhybridized DNA, the use of microliter sample volumes, and disposable transducers and, hence, offers great promise for decentralized genetic testing.