DNA sequencing by capillary array electrophoresis and microfabricated array systems

Carrilho, Emanuel

doi:10.1002/(sici)1522-2683(20000101)21:1<55::aid-elps55>3.0.co;2-i

Cited by 113 publications

(60 citation statements)

References 105 publications

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“…A number of reviews have appeared covering the use of sieving polymers and their applications in DNA sequencing (see, e.g., [43][44][45][46][47]). Although it is not well understood why some polymers are better sieving matrices than others, some general guidelines begin to emerge: the reader is referred to a trilogy by Heller [48][49][50], laying down some basic principles.…”

Section: Dna Sequencingmentioning

confidence: 99%

Recent progress in DNA analysis by capillary electrophoresis

Righetti¹,

Gelfi²,

D’Acunto³

2002

Electrophoresis

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A number of recent developments in DNA analysis by capillary electrophoresis are here reviewed. They include capillary arrays for fast, parallel DNA sequencing as well as microfabricated capillary arrays. Microfluidic chips for DNA sizing and quantitation are also covered, as well as microdevices containing arrays of regular obstacles acting as size-separators during DNA migration. Screening of DNA point mutations by two much improved techniques is also reported: in one case, such mutations are detected (but only on relative short, ca. 60-70 base-long fragments) by free electrophoresis in rather acidic (pH ca. 3) buffers; in the case of single-strand chain polymorphism, an improved technique is described based on near-neutral pH buffers with mixtures of Tris/MES cations/zwitterions. When studying the behavior of inorganic and organic cations in the Debye-Hückel layer of DNA, it was found that the latter (especially a large number of Good's buffers and other zwitterions, such as His) would bind to the DNA filament not only via charge interaction, but also via additional bonds, notably hydrogen bonds, thus altering the electrophoretic (and possibly the biological) behavior of DNA molecules. However, whether or not borate ions would bind to DNA remains still an unsettled question. Finally, capillary electrophoresis was found to be instrumental in measuring fine physicochemical parameters pertaining to DNA polyelectrolytes, such as their free mobility and their translational diffusion coefficients.

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Section: Dna Sequencingmentioning

confidence: 99%

Recent progress in DNA analysis by capillary electrophoresis

Righetti¹,

Gelfi²,

D’Acunto³

2002

Electrophoresis

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“…These microfluidic devices can be fabricated using a variety of substrate materials, with several molecular biology processes integrated onto a single device (e.g., lab-on-a-chip). A number of reviews have been devoted to microfluidic devices (Becker and Gartner 2000;Carrilho 2000;McDonald et al 2000;Quake and Scherer 2000;Boone et al 2002;Paegel et al 2003;Kan et al 2004), recent advances of which I will highlight as they relate to DNA sequencing. These miniature devices have several advantages over CAE, including improved sample injection and faster separation times.…”

Section: Microfluidic Separation Platformsmentioning

confidence: 99%

Emerging technologies in DNA sequencing

Metzker¹

2005

Genome Res.

413

262

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Demand for DNA sequence information has never been greater, yet current Sanger technology is too costly, time consuming, and labor intensive to meet this ongoing demand. Applications span numerous research interests, including sequence variation studies, comparative genomics and evolution, forensics, and diagnostic and applied therapeutics. Several emerging technologies show promise of delivering next-generation solutions for fast and affordable genome sequencing. In this review article, the DNA polymerase-dependent strategies of Sanger sequencing, single nucleotide addition, and cyclic reversible termination are discussed to highlight recent advances and potential challenges these technologies face in their development for ultrafast DNA sequencing.

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“…Many techniques developed in traditional CE have been transferred onto microchip CE with appropriate modifications [3][4][5][6][7]. Multilane microchips have been developed to obtain high throughput analysis and were applied in DNA sequencing, genotyping, pharmaceuticals and other areas [8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

Frontal analysis in microchip CE: A simple and accurate method for determination of protein–DNA dissociation constant

et al. 2007

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Equilibrium constants, such as the dissociation constant (K d ), are a key measurement of noncovalent interactions that are of importance to the proper functioning of molecules in living systems. Frontal analysis (FA) is a simple and accurate capillary electrophoresis (CE) method for the determination of K d . Microchip CE coupled with laser-induced fluorescence (LIF) detection was used to determine K d of protein-DNA interactions using the FA method. A model system of immunoglobulin E (IgE) and the IgE-binding aptamer was selected to demonstrate the capability of FA in microchip CE. Because the fluorescence emission was dependent on the dye migration velocity, the velocity of the free aptamer was adjusted to be the same as that of the aptamer-IgE complex by setting up individual separation voltage configurations for the free and bound aptamers. The ratio of the free and bound aptamers in the equilibrium mixture was directly measured from the heights of their plateaus detected at 1.0 cm from the intersection of the microchip, and no internal standard was needed. The K d of the IgE-aptamer pair was determined as 6 ± 2 nM which is consistent with the reported results (8 nM).

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DNA sequencing by capillary array electrophoresis and microfabricated array systems

Cited by 113 publications

References 105 publications

Recent progress in DNA analysis by capillary electrophoresis

Recent progress in DNA analysis by capillary electrophoresis

Emerging technologies in DNA sequencing

Frontal analysis in microchip CE: A simple and accurate method for determination of protein–DNA dissociation constant

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