DNA sequencing in a monolithic microchannel device

Abstract

We present 50 cm long microchannels in a monolithic device for high resolution, long read-length DNA sequencing. These devices were fabricated and bonded in borofloat glass using unconventional photolithography techniques with 48-188 independent, straight microchannels. The microchannel DNA separation was tested with POP-6 polymer and a DNA sequencing ladder separated at room temperature and 200 V/cm. Single-base resolution greater than 600 bases was achieved and the sequence base called to 640 bases with 98% accuracy. Under the same experimental conditions, the performance of the microchip was identical to a fused-silica capillary with similar cross-sectional area.

Peer Reviewed: Plastic Advances Microfluidic Devices

“…Microfabrication using these inorganic materials is quite inexpensive when chip sizes are small (~1 cm 2 ), but when making the larger fluidic devices (~100 cm 2 ) required for DNA sequencing or parallel screening of many pharmaceutical candidates (1), costs become prohibitive.…”

“…Interestingly, we observe that the background fluorescence is only slightly higher than with a glass microfluidic device of similar thickness when our acrylic chips are excited by 488-nm laser light under photobleaching conditions. Several groups have investigated electrochemical detection as an alternative to fluorescence (1,3,6,7 ). Rossier et al integrated carbon microband electrodes into the bottom-or sidewalls of rectangular microchannels in plastics and demonstrated a detection limit of ~1 fmol for ferrocenecarboxylic acid (7 ).…”

“…Capillary bundles filled with high-molecular-weight sieving polymers such as linear polyacrylamide provide rapid, high-resolution separations and automated capillary filling. In the future, it is likely that capillary arrays will be replaced by even larger arrays of microchannels fabricated in planar substrates to form highly multiplexed microfabricated DNA sequencers (1,10). The potential to integrate additional functionalities onto such systems-such as onchip purification of the sample prior to CE sequencing-offers the hope that the manual operations that currently account for over half the cost of obtaining a DNA sequence can be automated.…”

Fast High-throughput Screening of the H1N1 Virus by Parallel Detection with Multi-channel Microchip Electrophoresis

“…[13][14][15][16][17][18] However, using single capillaries in conventional CE limits its throughput; therefore, by incorporating many capillaries into a single CE instrument, the capillary array electrophoresis (CAE) system was developed to increase throughput. 19 However, as the number of capillaries increases, it becomes more difficult to control the injection of the sample and to simultaneously detect signals from all of the capillaries.…”

Highly efficient separation of dsDNA fragments on glass chips by using an ultralow viscosity sieving matrix

“…The first successful efficient separation of dsDNA fragments on electrophoresis microchips was achieved in a cellulose derivative by Woolley [3]. Since then, microchip-based electrophoresis has made rapid advances in DNA analysis, such as PCR products [4 -6], double-stranded DNA fragments [3,7], and the sequencing of DNA [8,9], due to its high performance, speed, and resolution.…”