DNA Sequencing on Microfabricated Electrophoretic Devices

Schmalzing, Dieter; Adourian, Aram; Koutny, Lance; Ziaugra, Liuda; Matsudaira, Paul; Ehrlich, D. J.

doi:10.1021/ac971381a

Cited by 220 publications

(183 citation statements)

References 28 publications

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“…Thus, to obtain reasonable read lengths (the number of nucleotide bases resolved in a single electrophoretic run) for DNA sequencing, long separation channels are required. For example, for a read length of 500 bases in a 4% polyacrylamide gel, the channel length must be 28 cm (26).…”

Section: Applicationsmentioning

confidence: 99%

Peer Reviewed: Polymeric Microelectromechanical Systems.

Soper¹,

et al. 2000

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Section: Applicationsmentioning

confidence: 99%

Peer Reviewed: Polymeric Microelectromechanical Systems.

Soper¹,

et al. 2000

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“…In subsequent work, the classical variables of DNA sequencing separations such as column length, sieving matrix composition, injection parameters, etc. have been explored and optimized (13,14), producing read lengths as long as 800 bp for a 40-cm-long microfabricated capillary in 80 min (15).Microfabricated capillary array electrophoresis ( CAE) devices are advantageous compared with drawn capillary array instrumentation because they allow monolithic array construction, precise definition of picoliter sample injection plugs, and the potential for integrated, low volume sample processing. Our group has pioneered the design and construction of microfabricated capillary array electrophoresis devices demonstrating rectilinear networks of 12 and 48 channels for parallel DNA fragment analysis (16, 17).…”

mentioning

confidence: 99%

High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor

Paegel

Emrich

Wedemayer

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

249

179

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High throughput DNA sequencing has been performed by using a microfabricated 96-channel radial capillary array electrophoresis ( CAE) microchannel plate detected by a 4-color rotary confocal fluorescence scanner. The microchannel plate features a novel injector for uniform sieving matrix loading as well as high resolution, tapered turns that provide an effective separation length of 15.9 cm on a compact 150-mm diameter wafer. Expanded common buffer chambers for the cathode, anode, and waste reservoirs are used to simplify electrode addressing and to counteract buffering capacity depletion arising from the high electrophoretic current. DNA sequencing data from 95 successful lanes out of 96 lanes run in parallel were batch-processed with BASEFINDER, producing an average read length of 430 bp (phred q > 20). Phred quality values were found to exceed 40 (0.01% probability of incorrectly calling a base) for over 80% of the read length. The CAE system demonstrated here produces sequencing data at a rate of 1.7 kbp͞min, a 5-fold increase over current commercial capillary array electrophoresis technology. Additionally, this system permits lower reagent volumes and lower sample concentrations, and it presents numerous possibilities for integrated sample preparation and handling. The unique capabilities of CAE technology should make it the next generation, high performance DNA sequencing platform.A dvances in DNA sequencing technologies over the past decade have been driven by the Human Genome Project (1). To achieve the ambitious goals of the genome project, sequencing centers replaced slab gel-based systems with capillary array electrophoresis (CAE) instruments that are based either on the scanning confocal detector developed in our laboratory (2, 3) or on sheath-flow detection (4, 5). Although the draft sequence of the human genome is now ''complete'' (6), expanded sequencing capacity is still required for the characterization of human sequence variation and for sequencing other genomes. In pursuing these goals, many technology development efforts are focused on the use of microfabricated electrophoretic analysis systems.Microfabricated capillary electrophoresis devices were introduced by Manz and coworkers (7,8) in the early 1990s. These microchips efficiently and very rapidly separated mixtures of fluorescent dyes and fluorescently labeled amino acids by using a fraction of the conventionally required capillary length. Initial experiments were rapidly followed by the demonstration of protocols for rapid DNA sizing and sequencing (9, 10), integrated thermal cycling fluidic circuitry (11), and clinically relevant genotyping (12). In subsequent work, the classical variables of DNA sequencing separations such as column length, sieving matrix composition, injection parameters, etc. have been explored and optimized (13,14), producing read lengths as long as 800 bp for a 40-cm-long microfabricated capillary in 80 min (15).Microfabricated capillary array electrophoresis ( CAE) devices are advantageous compared with drawn cap...

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“…PAA-coated microchannels generated according to the Hjertén procedure have also been applied in MCE to enable DNA separations [68][69][70][71][72][73]. In the aforementioned articles, PAA-coated glass devices have been used in combination with polyacrylamide as sieving matrix for DNA separations; however, no additional data on the performance of the coatings were given.…”

Section: Polyacrylamidementioning

confidence: 99%

Surface modification in microchip electrophoresis

2003

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Different approaches and techniques for surface modification of microfluidic devices applied for microchip electrophoresis are reviewed. The main focus is on the improved electrophoretic separation by reducing analyte-wall interactions and manipulation of electroosmosis. Approaches and methods for permanent and dynamic surface modification of microfluidic devices, manufactured from glass, quartz and also different polymeric substrates, are described.

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DNA Sequencing on Microfabricated Electrophoretic Devices

Cited by 220 publications

References 28 publications

Peer Reviewed: Polymeric Microelectromechanical Systems.

Peer Reviewed: Polymeric Microelectromechanical Systems.

High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor

Surface modification in microchip electrophoresis

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