High-Throughput Single-Molecule DNA Screening Based on Electrophoresis

Shortreed, Michael R.; Li, Hanlin; Huang, Weian; Yeung, Edward S.

doi:10.1021/ac991428n

Cited by 74 publications

(92 citation statements)

References 26 publications

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“…Presently, the design of such vector, micropatterned separation chips lacks a rational basis, with much of the pertinent literature reporting only construction techniques and observed experimental separation efficiencies for a given pattern, solute-solvent system, and set of operating conditions [3,7,10]. Several theoretical explanations of the separation characteristics of micropatterned devices have been proposed [9,11], but they are fundamentally irrational owing to their ad hoc incorporation of diffusion effects, as well as in the inappropriate implicit assumption of position-independent and isotropic mobilities at the interstitial-(i.e.…”

mentioning

confidence: 99%

“Vector Chromatography”: Modeling Micropatterned Separation Devices

Dorfman

Brenner

2001

Journal of Colloid and Interface Science

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A repetitive sequence of quiescent fluid layers of differing viscosities through which small spherical Brownian particles move is analyzed so as to illustrate in a simple context how the theory of macrotransport processes, a generalization of Taylor dispersion theory, may be employed to rigorously analyze spatially periodic micropatterned chromatographic separation devices for circumstances in which the solute species to be separated are animated by the action of species-specific external forces oriented asymmetrically relative to the body-fixed pattern. In the generic "vector" separation scheme, illustrated by our elementary example, the different species undergoing separation move, on average, in different directions relative to pattern-fixed axes, whence their chromatographic sorting is effected according to their different mean angular trajectories through the device. This scheme differs fundamentally from traditional "scalar" chromatographic separation schemes, wherein all species move on average parallel to the animating force (including circumstances in which they are passively entrained in a unidirectional solvent flow) and hence for which the sorting is effected by the relative speeds of the several species through the chromatographic column.Vector chromatography is quantified by two global "macrotransport coefficients," namely the solute mobility dyadic M * (representing the tensor proportionality coefficient between the mean solute velocity vector U * and the external force vector F acting upon the solute molecules) and the dispersivity dyadic D * (resulting from the deviation of the instantaneous position of the particle from its mean position based upon its mean velocity vector). In the present example these coefficients are studied parametrically as functions of: (i) the orientation of the external force relative to the symmetry axis of the fluid layers; (ii) the local viscosity distribution within a layer; (iii) the vector particle Peclet number (constructed from the vector force, the length of the viscosity period, and the Boltzmann factor kT ); and (iv) the thermodynamic interphase solute partition distribution coefficient between the two fluid layers comprising a unit cell.

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confidence: 99%

“Vector Chromatography”: Modeling Micropatterned Separation Devices

Dorfman

Brenner

2001

Journal of Colloid and Interface Science

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“…This velocity determination method was called the streak method. 14 It is clear that the trace lengths of different microbeads are obviously various. We followed 30 microbeads excited with wide field mode and calculated their velocities in every frame.…”

Section: Resultsmentioning

confidence: 99%

“…SMD has been applied for monitoring molecular diffusion in free solutions, 9 studying absorption and desorption of protein molecules at a solid/liquid interface, 10,11 finding anomalous radial migration of DNA molecules in capillary electrophoresis. 12,13 In addition to fundamental investigations, SMD has been extensively applied for biological or biochemical areas, such as high throughput DNA screening in electrophoresis, 14,15 single molecule immunoassay, 16 DNA sizing and sorting, [17][18][19][20] DNA mapping 21,22 and in situ hybridization. 23 The single molecule detection technique was also used to probe the flow profile.…”

Section: Introductionmentioning

confidence: 99%

Simultaneous measurements of the flow velocities in a microchannel by wide/evanescent field illuminations with particle/single molecules

et al. 2005

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A laser-induced fluorescence imaging method was developed to simultaneously measure flow velocities in the middle and near wall of a channel with particles or single molecules, by selectively switching from the wide field excitation mode to the evanescent wave excitation mode. Fluorescent microbeads with a diameter of 175 nm were used to calibrate the system, and the collisions of microbeads with channel walls were directly observed. The 175 nm microbeads velocities in the main flow and at 275 nm from the bottom of the channel were measured. The measured velocities of particles or single molecules in two positions in a microchannel were consistent with the calculated value based on Poiseuille flow theory when the diameter of a microbead was considered. The errors caused by Brownian diffusion in our measurement were negligible compared to the flow velocity. Single lDNA molecules were then used as a flowing tracer to measure the velocities. The velocity can be obtained at a distance of 309.0 ¡ 82.6 nm away from bottom surface of the channel. The technique may be potentially useful for studying molecular transportation both in the center and at the bottom of the channel, and interactions between molecules and microchannel surfaces. It is especially important that the technique can be permitted to measure both velocities in the same experiment to eliminate possible experimental inconsistencies.

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“…[11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] Several types of chips has been introduced for the postgenomic researches such as DNA/RNA chips [28][29][30][31] and the serial analysis of gene expression. [32][33][34][35] The viscosity of the separation media is one important factor for chip separation since the bounded microfluidic devices can not withstand high loading pressure.…”

Section: Introductionmentioning

confidence: 99%

Low Viscous Separation Media for Genomics and Proteomics Analysis on Microchip Electrophoresis System

Jabasini

Murakami

Kaji

et al. 2006

Biological & Pharmaceutical Bulletin

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Microchip electrophoresis has widely grown during the past few years, and it has showed a significant result as a strong separation tool for genomic as well as proteomic researches. To enhance and expand the role of microchip electrophoresis, several studies have been proposed especially for the low viscous separation media, which is an important factor for the success of microchip with its narrow separation channels. In this paper we show an overview for the done researches in the field of low viscous media developed for the use in microchip electrophoresis. For genomic separation studies polyhydroxy additives have been used enhance the separation of DNA at low polymer concentration of HPMC (Hydroxypropylmethyl cellulose) which could keep the viscosity low. Mixtures of poly(ethylene oxide) as well as Hydroxyporpyl cellulose have been successfully introduced for chip separation. Furthermore high molecular mass polyacrylamides at low concentrations have been studied for DNA separation. A mixture of polymer nanoparticle with conventional polymers could show a better resolution for DNA at low concentration of the polymer. For the proteomic field isoelectric focusing on chip has been well overviewed since it is the most viscous separation media which is well used for the protein separation. The different types of isoelectric focusing such as the ampholyte-free type, the thermal type as well as the ampholyte-depended type have been introduced in this paper. Isoelectric focusing on chip with its combination with sodium dodecyl sulfate (SDS) page or free solution could give a better separation. Several application for this low viscous separation medias for either genomic or proteomic could clearly show the importance of this field.

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High-Throughput Single-Molecule DNA Screening Based on Electrophoresis

Cited by 74 publications

References 26 publications

“Vector Chromatography”: Modeling Micropatterned Separation Devices

“Vector Chromatography”: Modeling Micropatterned Separation Devices

Simultaneous measurements of the flow velocities in a microchannel by wide/evanescent field illuminations with particle/single molecules

Low Viscous Separation Media for Genomics and Proteomics Analysis on Microchip Electrophoresis System

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