Capillary gel electrophoresis with sinusoidal voltammetric detection: a strategy to allow four-"color" DNA sequencing.

A novel detection strategy for DNA sequencing applications that utilizes a frequency-based electrochemical method is reported. Sinusoidal voltammetry is used to selectively identify four unique redox molecules that are covalently attached to the 5'-end of a 20-base sequencing primer. The tags used in this work are ferrocene derivatives with different substituents attached to the ferrocene ring, where the electron-donating or -withdrawing character of the substituent alters the half-wave potential of the modified ferrocene. Therefore, each tag has a unique SV frequency spectrum that can be easily identified in the frequency domain. In this work, the discrimination of one tag versus all others is accomplished through a "phase-nulling" technique. The signal for each tag is selectively eliminated while the other three responses remain virtually unchanged. This analysis scheme allows for the selective identification of each tagged oligonucleotide eluting in sieving polymer capillary gel electrophoresis with a separation efficiency of 2 x 10(6) theoretical plates per meter. This separation efficiency is sufficient to perform "low-resolution" DNA sequencing; the conditions used in this work have not yet been optimized for high-resolution sequencing applications.

Immobilization and detection of DNA on microfluidic chips.

With the rapid development of micro-Total Analysis Systems (muTAS) and sensitive DNA recognition technologies, it is possible to immobilize DNA probes to small areas of surfaces other than silicon. To this end, photolithographic techniques were used to derivatize micron-sized, spatially segregated DNA recognition elements in Polydimethylsiloxane (PDMS) microfluidic structures. UV light was used to initiate attachment of a photoactive biotin molecule to the substrate surface. Once biotin was attached to a substrate, biotin/avidin/biotin chemistry was used to attach fluorescently labeled or non-labeled avidin and biotinylated DNA probes. These techniques were applied to create a prototype microfluidic sensor device that was used to separate and identify synthetic DNA targets that were fluorescently-labeled.

Detection of native amino acids and peptides utilizing sinusoidal voltammetry.

Native amino acids and peptides were detected at a copper microelectrode using sinusoidal voltammetry (SV). Traditionally, these molecules can only be measured after derivatization with either a fluorescent or electroactive tag. In this work, an electrocatalytic oxidation reaction at copper is used to detect underivatized peptides and amino acids. The oxidation reaction is somewhat independent of peptide structure (i.e., it is not limited to the detection of aromatic amino acids) and is therefore able to produce nanomolar detection limits for all amino acids and peptides tested. A scanning technique, sinusoidal voltammetry, is used to provide the sensitivity of constant-potential techniques but also provide selectivity gained through utilization of the frequency domain. The frequency spectrum due to the oxidation of each molecule has a unique "fingerprint" response resulting from the kinetics of oxidation at the electrode surface. Through examination of the frequency spectra, even structurally similar molecules can be easily distinguished from one another. Flow injection analysis is used to demonstrate the sensitive and selective detection of a variety of amino acids and peptides. This technique can also be easily coupled to a separation step, i.e., high-performance liquid chromatography or capillary electrophoresis without electrode fouling from the adsorption of the analytes.

Laser interference pattern ablation of a carbon fiber microelectrode: biosensor signal enhancement after enzyme attachment.

Fluorescence microscopy was used to visualize the accumulated fluorescent product of the enzyme alkaline phosphatase to indicate where active covalently bound enzyme remained on the surface after application of a Nd: YAG laser interference pattern to a surface that was first globally derivatized with the covalently bound enzyme. The electrochemical kinetics of the same carbon fiber surface were examined through the electrogenerated chemiluminescence of Ru(bpy)(3)2+ to determine that electron-transfer sites were indeed segregated from the enzyme-binding sites. The enzyme-derivatized areas are determined to be separate and distinct from the areas of enhanced electron transfer. Two other enzymes, glucose oxidase and malic dehydrogenase, were then covalently bound to carbon fiber microelectrode surfaces in order to verify the change in detection limit of their respective cofactors, NADH or H2O2, under a variety of surface conditions. The S/N of an enzyme-modified electrode after laser interference pattern photoablation and electrocatalytic treatment is improved by more than 1 order of magnitude over that observed at an electrode that is globally enzyme modified.

Segregation of micrometer-dimension biosensor elements on a variety of substrate surfaces.

With the rapid development of micro total analysis systems and sensitive biosensing technologies, it is often desirable to immobilize biomolecules to small areas of surfaces other than silicon. To this end, photolithographic techniques were used to derivatize micrometer-sized, spatially segregated biosensing elements on several different substrate surfaces. Both an interference pattern and a dynamic confocal patterning apparatus were used to control the dimensions and positions of immobilized regions. In both of these methods, a UV laser was used to initiate attachment of a photoactive biotin molecule to the substrate surfaces. Once biotin was attached to a substrate, biotin/avidin/biotin chemistry was used to attach fluorescently labeled or nonlabeled avidin and biotinylated sensing elements such as biotinylated antibodies. Dimensions of 2-10 microm were achievable with these methods. A wide variety of materials, including glassy carbon, quartz, acrylic, polystyrene, acetonitrile-butadiene-styrene, polycarbonate, and poly(dimethylsiloxane), were used as substrates. Nitrene- and carbene-generating photolinkers were investigated to achieve the most homogeneous films. These techniques were applied to create a prototype microfluidic sensor device that was used to separate fluorescently labeled secondary antibodies.

Micrometer dimension derivatization of biosensor surfaces using confocal dynamic patterning.

Using laser scanning confocal optics in conjunction with avidin/biotin technology, micrometer-sized patterns of biomolecules were fabricated on glassy-carbon and fused-silica surfaces. Photoactive biotin was immobilized using the 325-nm line of a Helium-Cadmium laser, which was focused through a 25x or 100x quartz microscope objective. A three-dimensional piezoelectric micromanipulator was used to position the sample surface in the focal plane of the microscope objective and to create patterns on the focused surface. Biotin patterns with line widths of 5-20 microns were produced by varying the scan speed of the micromanipulator while exposing the surface to the laser. The integrity of the immobilized biotin was confirmed by subsequent derivatization with fluorescently labeled avidin. Fluorescence microscopy with a cooled charge coupled device (CCD) imaging system was used to visualize the distribution of biotin and fluorescent avidin within the patterns created by the laser.

Separation of double- and single-stranded DNA restriction fragments: capillary electrophoresis with polymer solutions under alkaline conditions.

Capillary electrophoresis in buffers containing hydroxyethyl cellulose (HEC) was used to separate double- and single-stranded DNA restriction fragments under neutral and alkaline conditions in epoxy-coated capillaries. It was found that better resolution was achieved using highly entangled HEC solutions for a narrow range of DNA fragment sizes, while lower resolution was obtained over a wide separation range using diluted HEC solutions. Optimal resolution of these DNA fragments was obtained using buffers containing 0.5% HEC at pH 11 with plate numbers exceeding 3 x 10(6) plates/m. It was also found that the diffusion coefficients and electrophoretic mobilities of DNA fragments decreased with increasing pH. This may indicate a more extended DNA conformation and, therefore, enhancement of transient entanglement coupling between DNA and HEC polymers under alkaline condition. At pH 12, ss-DNA were well separated in entangled HEC solutions; however, the resolution of ss-DNA was significantly decreased in diluted polymer solution.

Preservation of NADH voltammetry for enzyme-modified electrodes based on dehydrogenase.

Minimizing overpotential and generating high faradaic currents are critical issues for fast-scan voltammetry of beta-nicotinamide adenine dinucleotide (NADH) for the sensitivity of enzyme-modified electrodes based on dehydrogenases. Although NADH voltammetry exhibits high overpotential and poor voltammetric peak shape at solid electrode surfaces, modification of the electrode surface can improve the electrochemical response at carbon fibers. However, these improvements are severely degraded upon the covalent attachment of enzyme. The creation of improved electron-transfer properties and the retention of these properties throughout the enzyme attachment process is the focus of this study. A novel polishing and electrochemical pretreatment method was developed which generated a decreased overpotential and a high faradaic current at carbon-fiber electrodes for NADH. Factors that lead to a degradation of voltammetric response during the enzyme fabrication were investigated, and both the aging and the covalent modification of the pretreated surface contributed to this degradation. Attachment processes that minimized the preparation time, in turn, maximized the retention of the facile electron-transfer properties. These attachment processes included varying the surface attachment reactions for the enzyme. Preparation time reduction techniques included modeling existing techniques and then improving kinetic and mass transport issues where possible. Alternate covalent attachment methods included a direct electrochemical amine reaction and an electrochemically reductive hydrazide reaction. The surface attachment and retention of electron-transfer properties of these probes were confirmed by fluorescence and electrochemical studies.

Development of sub-micron patterned carbon electrodes for immunoassays.

Sub-micron sized domains of a carbon surface are derivatized with antibodies using biotin/avidin technology. These sites are spatially-segregated from, and directly adjacent to, electron transfer sites on the same electrode surface. The distance between these electron transfer sites and enzyme-loaded domains are kept to a minimum (e.g. less than a micron) to maintain the high sensitivity required for the measurement of enzyme-linked cofactors in an enzyme-linked immunoassay (ELISA). This is accomplished through the use of photolithographic attachment of photobiotin using an interference pattern from a UV laser generated at the electrode surface. This allows the construction of microscopic arrays of active ELISA sites on a carbon substrate while leaving other sites underivatized to facilitate electron transfer reactions of redox mediators; thus maximizing sensitivity and detection of the enzyme mediator. The carbon electrode surface is characterized with respect to its chemical structure and electron transfer properties following each step of the antibody immobilization process. The characterization of specific modifications of micron regions of the carbon surface requires analytical methodology that has both high spatial resolution and sensitivity. We have used fluorescence microscopy with a cooled CCD imaging system to visualize the spatial distribution of enzyme immobilization sites (indicated by fluorescence from Texas-Red labeled antibody) across the carbon surface. The viability of the enzyme attached to the surface in this manner was demonstrated by imaging the distribution of an insoluble, fluorescent product.

Localized avidin/biotin derivatization of glassy carbon electrodes using SECM.

Different forms of the microreagent mode of SECM were used to attach biotin or make "clean" spots on micron-sized regions on the surface of a carbon electrode. In the direct-write mode, the SECM probe tip is used as an electrochemical "pen" depositing biotin in micron-sized lines on the carbon substrate as it is scanned across its surface. In the negative microreagent mode, the SECM probe tip is used as an electrochemical "eraser" cleaning of the surface attached molecules and leaving clean spots on the surface of a globally derivatized carbon surface. This type of simple micromodification of the surface of a carbon electrode will allow the fabrication of biosensors that can potentially be tailor-made for a variety of applications.

A laser ablation method for the spatial segregation of enzyme and redox sites on carbon fiber microelectrodes.

A laser-generated interference pattern was used to remove enzyme from micrometer-wide stripes on an enzyme-covered carbon fiber microelectrode surface to create regions of facile electron transfer. Fluorescence microscopy was used to visualize fluorophore-tagged enzyme to indicate where the adsorbed enzyme remained on the surface. The electrochemical kinetics of the carbon fiber surface were examined to see if electron-transfer sites could indeed be segregated from enzyme adsorbed across the entire surface. CCD imaging of the electrochemical luminescence of Ru(bpy)3(2+) was used to verify the segregation between photoablated sites (with facile electron-transfer kinetics) and surfaces with adsorbed enzyme (which exhibit slow electron-transfer kinetics). The laser-ablated surface could also be distinguished from the enzyme-covered carbon surface with atomic force microscopy. Thus, photoablation of the surface of a protein-covered carbon fiber microelectrode with an interference pattern generated by a Nd:YAG laser allows the activation of 1.7-micron-wide bands of the electrode surface (available for facile electron transfer) while leaving 2.6-micron-wide enzyme-modified areas intact, thereby producing electroactive regions directly adjacent to enzyme modified regions of the same surface.

Background-subtraction of fast-scan cyclic staircase voltammetry at protein-modified carbon-fiber electrodes.

Background-subtraction techniques were applied to the voltammetry of nicotinamide adenine dinucleotide (NADH) at protein-modified carbon-fiber microelectrodes. The background currents at carbon-fiber electrodes were stable and voltammetric scans immediately before or after the analyte were effectively used for background subtraction. Digital step-potential waveforms were used to excite these carbon-fiber electrodes, where the resulting voltammetric analysis assessed the optimal switching and initial potentials and the electrochemical response time was determined. The initial potential was 0.0 V and the switching potential 1.1 V (versus Ag/AgCl) and the response time was approximately 300 ms. Some sensitivity to NADH was lost and voltammetric prescans were required at protein-modified electrodes to obtain a stable baseline. Current versus time was assessed by the average current of the faradaic region from each voltammogram and by differential current; the average current minus the current from a non-faradaic potential range. Differential current assessments discriminated against artifacts caused by pH (as high as 1.0 pH unit) and ionic strength flux (100 mM). These background-subtraction techniques allowed the faradaic information to be obtained quickly and conveniently while maximizing sensitivity and maintaining selectivity.

Electron transfer kinetics at a biotin/avidin patterned glassy carbon electrode.

Photolithographic techniques using a laser interference pattern were used to attach photobiotin to micron-sized stripes on the surface of a carbon electrode. Fluorophore-tagged avidin was attached to this spatially-patterned biotin with essentially no loss in spatial resolution. The kinetics of the glassy carbon surface were examined to see if electron transfer sites could indeed be segregated from the attachment sites of photobiotin-immobilized avidin. The ECL of luminol and SECM were used to verify the segregation between underivatized sites (which exhibit normal electron transfer kinetics) and extensively derivatized biotin/avidin surfaces (which presumably exhibit slow electron transfer kinetics). Both techniques were found to be capable of differentiating the protein-covered surface from bare carbon with sufficient resolution to tell whether a significant portion of the carbon surface is still active and available to detect the product of an enzyme generated analyte. These results indicate that extensive biotin/avidin derivatization of the surface does decrease the electron transfer rate of a carbon electrode, and that the photolithographic approach was able to modify specific sections of the electrode surface, while leaving other regions untouched and available for facile electron transfer. This leads to a more general protocol for the construction of enzyme-based biosensors which utilize diffusable mediators.

Characterization of reaction dynamics in a trypsin-modified capillary microreactor.

Application of mild vibration to an immobilized trypsin capillary microreactor can enhance digestion rates for many globular and glycosylated proteins (12-70-kDa range) without additional sample handling. A sinusoid wave form generator and a simple piezoelectric transducer were used to apply vibration in a wide frequency range to the 50-µm-i.d. enzyme microreactor over its entire length. The mass transport properties of the microreactor were quantitatively examined for protein digestions through the use of an artificial globular protein. This was synthesized by covering the surface of 35-nm-diameter latex beads with a peptide (Leu-Arg-Leu). Capillary electrophoresis analysis of the microreactor products showed there were no mass transport-related effects for vibration of the capillary. Digestions of a range of globular protein structures were performed and the products analyzed by capillary electrophoresis. The rate enhancements were found to be related to the stability of the protein tertiary and secondary structure. Cytochrome c showed a dramatic acceleration in rate of digestion as the vibration frequency increased over a range of 200 Hz to 7.1 kHz. The ability to enhance reaction rates for very stable proteins can be gained by additional means of destabilizing the protein, as shown by removal of calcium from α-lactalbumin. Vibration of the enzyme capillary will have the greatest utility for extremely limited protein samples since chemical modification to completely denature proteins usually requires considerable sample handling.

Ultrasensitive voltammetric detection of underivatized oligonucleotides and DNA.

Electrochemical detection of nucleotides, ssDNA, and dsDNA was accomplished by using sinusoidal voltammetric detection at copper microelectrodes. Generally, detection of these molecules utilizes the electroactive nature of adenine and guanine residues at most electrode surfaces. The detection approach used in this study is based on the electrocatalytic oxidation of sugars and amines at copper surfaces. All nucleotides and DNA molecules comprise a ribose sugar backbone and primary amines present on the different nucleobases. Consequently, the detection approach is universal to all types of nucleotides. As the number of sugar moieties increases with the length of an oligonucleotide, the detection sensitivity is enhanced for bigger oligonucleotides. Irreversible adsorption of these oligonucleotides and other biomacromolecules like dsDNA on the electrode surface was avoided with sinusoidal voltammetry since it is a scanning electrochemical technique. The sensitivity of the detection strategy is, however, still preserved due to the effective decoupling of the faradaic signal from the capacitive background currents in the frequency domain. The ssDNA and dsDNA were detected in the picomolar concentration range. The electrochemical signal due to dsDNA is actually higher than that due to ssDNA due to the larger number of easily accessible sugars on the outer perimeter of a dsDNA double helix compared to those on a ssDNA of the same size. This is in contrast to the existing electrochemical detections techniques based on the electroactivity of the nucleobase.

Generation of biotin/avidin/enzyme nanostructures with maskless photolithography.

Micrometer-sized domains of a carbon surface are modified to allow derivatization to attach redox enzymes with biotin/avidin technology. These sites are spatially segregated from and directly adjacent to electron transfer sites on the same electrode surface. The distance between these electron transfer sites and enzyme-loaded domains must be kept to a minimum (e.g., less than 5 microns) to maintain the fast response time and high sensitivity required for the measurement of neurotransmitter dynamics. This is accomplished through the use of photolithographic attachment of photobiotin using an interference pattern from a UV laser generated at the electrode surface. This will allow the construction of microscopic arrays of active enzyme sites on a carbon fiber substrate while leaving other sites underivatized to facilitate electron transfer reactions of redox mediators, thus maximizing enzyme activity and detection of the enzyme mediator. The ultimate sensitivity of these sensors will be realized only through careful characterization of the carbon electrode surface with respect to its chemical structure and electron transfer properties following each step of the enzyme immobilization process. The characterization of specific modifications of micrometer regions of the carbon surface requires analytical methodology that has both high spatial resolution and sensitivity. We have used fluorescence microscopy with a cooled CCD imaging system to visualize the spatial distribution of enzyme immobilization sites (indicated by fluorescence from Texas Red-labeled avidin) across the carbon surface. The viability of the enzyme attached to the surface in this manner was demonstrated by imaging the distribution of an insoluble, fluorescent product. An atomic force microscope was used to obtain high-resolution images that probe the heterogeneity of the enzyme sites.

Direct electrochemical detection of purine- and pyrimidine-based nucleotides with sinusoidal voltammetry.

Sinusoidal voltammetry was employed to detect both purine- and pyrimidine-based nucleic acids. Adenine and cytosine, representing these two classes of nucleic acids, could be measured with submicromolar detection limits at a copper electrode under these conditions, where the sensitivity for adenine was much higher than that for cytosine. Detection limits for purine-containing nucleotides [e.g., adenosine 5'-monophosphate (AMP), adenosine 5'-diphosphate (ADP), and adenosine 5'-triphosphate (ATP)] were on the order of 70-200 nM using this method. These detection limits are achieved for native nucleotides and are over 2 orders of magnitude lower than those found with UV absorbance detection. Submicromolar detection limits were also obtained for pyrimidine-based nucleotides, which could also be detected with high sensitivity due to the presence of a sugar backbone that is electroactive at the copper surface. This detector is not fouled by the nucleotides and may be used for the sensitive detection of analytes eluting continuously in a flowing stream, i.e., from a chromatography column or an electrophoresis capillary.

Capillary biosensor for glutamate.

We have developed and characterized a novel glutamate biosensor which allows biological transduction of glutamate signal during transport of analyte from the sampling site to the detector. This biosensor exploits the high surface-to-volume ratio found in small-diameter fused silica capillaries. Glutamate dehydrogenase (GDH) was attached to the inner surface of a 75 µm i.d. capillary using biotin-avidin chemistry. In the presence of excess nicotinamide adenine dinucleotide (NAD(+)), GDH converts glutamate to α-ketoglutarate while simultaneously reducing NAD(+) to NADH. Detection of NADH was accomplished using laser-induced fluorescence. Perfusion with 30 µM glutamate in the presence of 3 mM NAD(+) resulted in a strong increase in fluorescence, with a response time of 450 ms. This effect was abolished upon exclusion of NAD(+) from the buffer. The limit of detection is 3 µM (S/N = 3), with a linear working range from 3 to 300 µM. Efficiency of the GDH-modified capillary ranged between 20% and 92% and was positively correlated with concentration of glutamate. The effect of linear velocity was also examined and was shown to be indirectly related to efficiency, with maximum response observed at 4.5 cm/min. In summary, we have demonstrated the successful attachment of glutamate dehydrogenase to the inner wall of a small-diameter fused silica capillary while retaining enzymatic activity. The resulting biosensor exhibits characteristics amenable for in vivo applications. Future efforts will be directed toward the incorporation of this biosensor into current technologies, such as capillary electrophoresis and microdialysis.

Electrocatalytic surface for the oxidation of NADH and other anionic molecules of biological significance.

A simple electrochemical treatment of a carbon fiber electrode surface has been found to dramatically improve the voltammetry of NADH and several other anionic molecules under steady-state and fast scan (100 V/s) conditions. The electrocatalytic surface is generated through the electrochemical oxidation of NADH on a carbon fiber electrode that exhibits product adsorption. The oxidative product is reacted with ascorbic acid at elevated temperatures to create a surface which has very little overpotential for the oxidation of dopamine and many metabolites such as NADH, DOPAC, uric acid, and ascorbate. The electrochemical properties of the modified surface were examined voltammetrically at both slow and fast scan rates. The surface shown in this paper shifts the oxidation overpotentials different magnitudes for each analyte tested, thus allowing discrimination between analytes of interest and their major interferences. Another benefit of this new electrocatalytic wave is that it decreases the limit of detection for NADH by approximately 1 order of magnitude. Therefore, this new carbon surface not only gives better discrimination between two analytes but also gives better detection limits for certain analytes of interest.