Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions

Ugaz, Victor M.; Elms, René D.; Lo, Roger C.; Shaikh, Faisal A.; Burns, Mark A.

doi:10.1098/rsta.2003.1365

Cited by 34 publications

(24 citation statements)

References 115 publications

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“…Reyes et al (2002) for a historical review). Electrokinetics plays the key role in many microfluidic separation and analysis devices (Bruin 2000;Verpoorte 2002;Lion et al 2003;Tegenfeldt et al 2004;Ugaz et al 2004), and interest in this classic subject has thus been renewed (Viovy 2000;Slater et al 2003;Stone, Stroock & Ajdari 2004;Squires & Quake 2005). In most cases, electrophoresis is used for separations.…”

Section: Introductionmentioning

confidence: 99%

Breaking symmetries in induced-charge electro-osmosis and electrophoresis

2006

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Building on our recent work on induced-charge electro-osmosis (ICEO) and electrophoresis (ICEP), as well as the Russian literature on spherical metal colloids, we examine the rich consequences of broken geometric and field symmetries upon the ICEO flow around conducting bodies. Through a variety of paradigmatic examples involving ideally polarizable (e.g. metal) bodies with thin double layers in weak fields, we demonstrate that spatial asymmetry generally leads to a net pumping of fluid past the body by ICEO, or, in the case of a freely suspended colloidal particle, translation and/or rotation by ICEP. We have chosen model systems that are simple enough to admit analysis, yet which contain the most important broken symmetries. Specifically, we consider (i) symmetrically shaped bodies with inhomogeneous surface properties, (ii) 'nearly symmetric' shapes (using a boundary perturbation scheme), (iii) highly asymmetric bodies composed of two symmetric bodies tethered together, (iv) symmetric conductors in electric-field gradients, and (v) arbitrarily shaped conductors in general non-uniform fields in two dimensions (using complex analysis). In non-uniform fields, ICEO flow and ICEP motion exist in addition to the more familiar dielectrophoretic forces and torques on the bodies (which also vary with the square of the electric field). We treat all of these problems in two and three dimensions, so our study has relevence for both colloids and microfluidics. In the colloidal context, we describe principles to 'design' polarizable particles which rotate to orient themselves and translate steadily in a desired direction in a DC or AC electric field. We also describe 'ICEO spinners' that rotate continuously in AC fields of arbitrary direction, although we show that 'near spheres' with small helical perturbations do not rotate, to leading order in the shape perturbation. In the microfluidic context, strong and steady flows can be driven by small AC potentials applied to systems containing asymmetric structures, which holds promise for portable or implantable self-powered devices. These results build upon and generalize recent studies in AC electro-osmosis (ACEO). Unlike ACEO, however, the inducing surfaces in ICEO can be physically distinct from the driving electrodes, increasing the frequency range and geometries available.

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Section: Introductionmentioning

confidence: 99%

Breaking symmetries in induced-charge electro-osmosis and electrophoresis

2006

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“…Many review articles have been published in recent years that focus on the various individual aspects of genetic analysis and DNA sequencing on microfluidic chips [32][33][34], and therefore we limit the discussion here to those systems that have succeeded in integrating two or more relevant functions into a single device. In principle, a totally integrated DNA sequencing platform could replace all robotics and other equipmentassociated with sample preparation as well as use microfabricated devices in place of CAE instruments to provide raw sequencing reads with substantially increased throughput.…”

Section: Microfabricated Systems For Genetic Analysismentioning

confidence: 99%

What is the future of electrophoresis in large‐scale genomic sequencing?

et al. 2006

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Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.

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“…One of the challenges for designing and constructing such devices comes from the need to achieve high-resolution separations over short distances in an easily interfaced and integrated system [11]. A strategy to achieve this goal is to increase throughput and reduce the fabrication expense by minimizing the size of a single device.…”

Section: Introductionmentioning

confidence: 99%

Effect of buffer flow on DNA separation in a microfabricated electrophoresis system

Chen

Burns

2005

Electrophoresis

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An adequate buffer reservoir is one essential component of an electrophoresis system, providing current carrying ions and maintaining constant pH. In a microfabricated DNA separation system with on-chip electrodes, the amount of buffer used is limited by the design of the device; the buffer continuity can be easily disturbed by the production of bubbles. Continuously flowing 1 x Tris-borate-EDTA (TBE) buffer over the electrodes at the cathodic end solves both problems. This flow increases the resolution for ssDNA primer separations (21 and 25 bases) to a maximum value of 1.4 within a distance of 1.2 cm, about four times higher than that without flow. Similar improvement has been achieved for dsDNA separation (20 bp ladder; BioRad) at a distance of only 0.4 cm, giving baseline resolution for bands from 20 to 240 bp. We have also investigated the effect of buffer concentration on resolution, and no similar improvement can be obtained by merely increasing the buffer concentration without flow.

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Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions

Cited by 34 publications

References 115 publications

Breaking symmetries in induced-charge electro-osmosis and electrophoresis

Breaking symmetries in induced-charge electro-osmosis and electrophoresis

What is the future of electrophoresis in large‐scale genomic sequencing?

Effect of buffer flow on DNA separation in a microfabricated electrophoresis system

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