Monolithic structures for integrated capillary electrophoresis systems.

Abstract

Since the early 1990's researchers have applied the principles of capillary electrophoresis to microfabricated devices. Separations of amino acids in free solutions as well as DNA in polymer solutions have been performed with high efficiencies in these devices. The majority of these devices have been fabricated using bulk micromachining of glass substrates and employ costly optical systems to detect fluorescent analytes. The real power of miniaturization is lost however, when these devices rely on a room full of equipment. This dissertation explores the use of surface micromachining for the fabrication of integrated capillary electrophoresis systems with on-chip fluorescence detection that can be incorporated into complex DNA diagnostic chips. A plastic surface micromachined technology is developed for the fabrication of long surface micromachined channels. This technology uses photoresist sacrificial layers in conjunction with vacuum deposited parylene-C. Channels up to 20 pm in height and nearly 2 mum in length have been fabricated. The low temperature fabrication process allows these channels to be fabricated on top of heaters, electrodes, photodiodes, temperature sensors, etc. without affecting device performance. Channels can be constructed on top of virtually any topography due to the conformal deposition of parylene-C. The channels fabricated show an extremely low autofluorescence as well as nearly 100% transparency, making them ideal for electrophoresis applications using fluorescence detection. Using this process electrophoresis devices fabricated on polycarbonate substrates are presented. A simple 4 mask process is developed that incorporates electrophoresis channels, electrodes, and reservoir structures. By using photodefinable silicone rubber for the reservoir structures, devices can be fabricated in a entirely batch manner. Steps typical in electrophoresis devices such as bonding, assembling of electrodes, and drilling of holes are replaced by surface micromachining. The use of lateral etch holes in long channels overcomes the limitations of sacrificially released channel structures. Separations of dsDNA in these devices have achieved over 100,000 theoretical plates. The use of plastics targets these devices for low cost, disposable DNA diagnostic applications. Finally, a monolithic surface micromachined electrophoresis device with integrated on-chip fluorescence detection is presented. An on-chip fluorescence detection system is developed using on-chip photodiodes, a thin film interference filter and a blue LED excitation source. DNA concentration levels of detection were as low as 225 pg/mul for dsDNA labeled with YOYO-1 intercalating dye. Separations of dsDNA were performed in these devices with on-chip DNA band detection. (Abstract shortened by UMI.)