The design, fabrication, and operation of a radial capillary array electrophoresis microplate and scanner for high-throughput DNA analysis is presented. The microplate consists of a central common anode reservoir coupled to 96 separate microfabricated separation channels connected to sample injectors on the perimeter of the 10-cm-diameter wafer. Detection is accomplished by a laser-excited rotary confocal scanner with four color detection channels. Loading of 96 samples in parallel is achieved using a pressurized capillary array system. High-quality separations of 96 pBR322 restriction digest samples are achieved in < 120 s with the microplate system. The practical utility and multicolor detection capability is demonstrated by analyzing 96 methylenetetrahydrofolate reductase (MTHFR) alleles in parallel using a noncovalent 2-color staining method. This work establishes the feasibility of performing high-throughput genotyping separations with capillary array electrophoresis microplates.

DNA sequencing separations have been performed in microfabricated electrophoresis channels with the goal of determining whether high-quality sequencing is feasible with these microdevices. The separation matrix, separation temperature, channel length and depth, injector size, and injection parameters were optimized. DNA fragment sizing separations demonstrated that 50-micron-deep channels provide the best sensitivity for our detection configuration. One-color sequencing separations of single-stranded M13mp18 DNA on 3% linear polyacrylamide (LPA) were used to optimize the twin-T injector size, injection conditions, and temperature. The best one-color separations were observed with a 250-micron twin-T injector, an injection time of 60 s, and a temperature of 35 degrees C. The first 500 bases appeared in 9.2 min with a resolution of > 0.5, and the separation extended to 700 bases. The best four-color sequencing separations were performed using 4% LPA, a temperature of 40 degrees C, and a 100-micron twin-T injector. These four-color runs were complete in only 20 min, could be automatically base-called using BaseFinder to over 600 bp after the primer, and were 99.4% accurate to 500 bp. These results significantly advance the quality of microchip-based electrophoretic sequencing and indicate the feasibility of performing high-speed genomic sequencing with microfabricated electrophoretic devices.

A new type of spectroelectrochemical sensor that demonstrates three modes of selectivity (electrochemistry, spectroscopy, and selective partitioning) is demonstrated. The sensor consists of an optically transparent electrode (OTE) coated with a selective film. Sensing is based on the change in the attenuation of light passing through the OTE that accompanies an electrochemical reaction of the analyte at the electrode surface. Thus, for an analyte to be detected, it must partition into the selective coating and be electrolyzed at the potential applied to the electrode, and either the analyte or its electrolysis product must absorb light at the wavelength chosen. Selectivity for the analyte relative to other solution components is obtained by choice of coating material, electrolysis potential, and wavelength for optical monitoring. The sensor concept is demonstrated with an OTE consisting of an indium−tin oxide coating on glass that has been over-coated with a sol−gel-derived charge-selective thin film. Attenuated total reflection (ATR) is used as the optical detection mode. The selective coating was an anionically charge-selective sol−gel-derived PDMDAAC−SiO2 composite film, where PDMDAAC = poly(dimethyldiallylammonium chloride). Fe(CN)6 4- was used as a model analyte to demonstrate that the change in the transmittance of the ATR beam resulting from oxidation of Fe(CN)6 4- to Fe(CN)6 3- can be used to quantify an analyte. The unoptimized sensor exhibited the following characteristics:  linear range, 8.0 × 10-6−5.0 × 10-5 M; sensitivity, 8.0 × 103ΔA/M; and detection limit, 8.0 × 10-6 M.

Three modes of selectivity based on charge-selective partitioning, electrolysis potential, and spectral absorption wavelength were demonstrated simultaneously in a new type of spectroelectrochemical sensor. Operation and performance of the three modes of selectivity for detection of analytes in the presence of direct interferences were investigated using binary mixture systems. These binary mixtures consisted of Fe(CN)(6)(3-) and Ru(bpy)(3)(2+) and of Fe(CN)(6)(4-) and Ru(CN)(6)(4)(-) in aqueous solutions. Results on the Fe(CN)(6)(3-)/Ru(bpy)(3)(2+) binary mixture showed that an anion-exchange coating consisting of PDMDAAC-SiO(2) [where PDMDAAC is poly(dimethyldiallylammonium chloride)] and a cation-exchange coating consisting of Nafion-SiO(2) can trap and preconcentrate analytes with charge selection. At the same time, such coatings exclude interferences carrying the same type of charge as that of the exchange sites in the sensor coating. Using the Fe(CN)(6)(4-)/Ru(CN)(6)(4-) binary mixture, the Fe(CN)(6)(4-) component can be selectively detected by restricting the modulation potential cycled to a range specific to the redox-active Fe(CN)(6)(4-) component and simultaneously monitoring the optical response at the overlapping wavelength of 420 nm. It was also shown that, when the wavelength for optical monitoring was chosen as 500 nm, which is specific to the Ru(CN)(6)(4-) component, interference from the Fe(CN)(6)(4-) component for spectroelectrochemical detection of Ru(CN)(6)(4-) was significantly suppressed, even though the cyclic modulation potential encompassed the redox range for the Fe(CN)(6)(4-) component.

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