Ultra-high-speed DNA fragment separations using microfabricated capillary array electrophoresis chips.

Abstract

Capillary electrophoresis arrays have been fabricated on planar glass substrates by photolithographic masking and chemical etching techniques. The photolithographically defined channel patterns were etched in a gass substrate, and then capillaries were formed by thermally bonding the etched substrate to a second glass slide. Highresolution electrophoretic separations of OX174 Hae m DNA restriction fragments have been performed with these chips using a hydroxyethyl cellulose sieving matrix in the channels. DNA fragments were fluorescently labeled with dye in the running buffer and detected with a laser-excited, confocal fluorescence system. The effects of variations in the electric field, procedures for injection, and sizes of separation and injection channels (ranging from 30 to 120 #m) have been explored. By use of channels with an effective length of only 3.5 cm, separations of #X174 Hae III DNA fragments from =70 to 1000 bp are complete in only 120 sec. We have also demonstrated high-speed sizing of PCR-amplified HLA-DQa alleles.This work establishes methods for high-speed, highthroughput DNA separations on capillary array electrophoresis chips.Capillary electrophoresis (CE) is a powerful method for DNA sequencing, forensic analysis, PCR product analysis, and restriction fragment sizing (1, 2). CE provides faster and higher-resolution separations than slab gel electrophoresis because higher electric fields can be applied. However, unlike slab gel electrophoresis, conventional CE allows analysis of only one sample at a time. Mathies and Huang (3) have introduced capillary array electrophoresis, in which separations are performed on an array of parallel silica capillaries, and demonstrated that it can be used to perform high-speed, high-throughput DNA sequencing (4, 5) and DNA fragment sizing (6). This method combines the fast electrophoresis times of CE with the ability to analyze multiple samples in parallel. The underlying concept behind the approach was to increase the information density in electrophoresis by miniaturizing the "lane" dimension to =-100 ,um. The further miniaturization of electrophoretic separations to increase the number of lanes, the speed, and the throughput would be valuable in helping to meet the needs of the Human Genome Project (7,8).The electronics industry routinely uses microfabrication to make circuits with features < 1 Aum in size. Microfabrication would allow the production of higher density capillary arrays, whose current density is limited by the capillary outside diameter (4-6). In addition, microfabrication of capillaries on a chip should make it feasible to produce physical assemblies not possible with glass fibers and to link capillaries directly to other devices on the chip. However, few devices for chemical separations have been made by microfabrication technology. A gas chromatograph (9) and a liquid chromatograph (10) have been fabricated on silicon chips, but these devices have not been widely used. Recently, several groups have fabricated individual CE devic...

Parallel molecular genetic analysis

“…Capillary technology also has the potential to be engineered on a microchip scale, decreasing electrophoresis times by an order of magnitude. [131][132][133] Mathies and co-workers developed a laser-excited, confocal fluorescence imaging system for DNA sequencing or mapping fragments in a planar array of several capillaries simultaneously, a technology known as capillary array electrophoresis (CAE). 134,135 CAE offers an excellent opportunity to develop instrumentation capable of striking increases in efficiency and convenience for DNA analysis.…”

Synthesis, Functionalization, and Design of Magnetic Nanoparticles for Theranostic Applications

“…[165] Later in the early 1990s, with the development of MF reactors which are the key components of a lab-on-a-chip (LOC) for use in synthetic chemistry, MF devices were used for chip-based separation. [166] Such MF reactors have played a significant role in improving the reaction conditions and production of chemicals. [167] In contrast with conventional batch systems, the use of MF to study and optimize the fabrication of a wide range of nanoparticles is attracting more and more attention [167] and their use for chemical synthesis gained a quick development with notable contributions from researchers at GlaxoSmithKline (UK), [168] Massachusetts Institute of Technology (USA), [169] the Institut für Mikrotechnik Mainz (Germany) [170] and Imperial College London (UK).…”

Applications of emerging technologies to the study of human genetics

“…3,4 The amplicons are then examined by chip capillary electrophoresis or other analyses on a chip. [5][6][7] Some of these approaches involve use of silicon-based technologies which have been previously confined to use in the semiconductor industry. 8 New materials like polycarbonate may soon expand the utility of this approach.…”