A new technology approach for the design, fabrication and application of an integrated free-solution capillary electrophoresis microsystem is presented. Combining the advantages of projection, contact photolithography and deep-reactive-ion-etching, this approach allows fast and flexible formation of micron-sized channels integrated with extremely high aspect-ratio (>50:1) sub-micron pillar arrays on a silicon substrate. Utilizing fluorescence video microscopy, free-solution DNA separation has been demonstrated. Furthermore, the detailed DNA molecular interaction with the pillars inside the microsystem can be analysed. In comparison with the previously reported fabrication technologies, such as electron beam lithography, the newly presented technology approach offers a significant improvement in fabrication time and design flexibility; both are highly desirable not only for potential commercialization of the free-solution electrophoresis microsystem in applications such as lab-on-a-chip but also for systematic studies of micro-scale DNA kinetics.

A capillary electrophoresis microsystem integrated with feed-through platinum electrodes was designed and fabricated for the separation of DNA fragments. A novel glass-to-silicon bonding technology, which allows anodic bonding of a glass wafer to a silicon wafer coated with a thick dielectric film by the inclusion of a thin intermediate amorphous silicon layer, was developed and employed to construct the microsystem. Despite the existence of a thick insulating material and non-uniform topography, robust devices without fluid leakage were obtained. Electrophoretic manipulation and separation of DNA fragments after capillary pre-treatment have been demonstrated and several operational considerations are discussed. The system performance suggests that silicon-based microsystems can be advantageous and practical for the fabrication of integrated microcapillary electrophoresis devices.

A study of the influences of embedding artificial structures in a microfluidic device for CE with a free buffer solution is presented. Compared with conventional slab-gel electrophoresis, three major additional effects on the overall system performance are identified when sub-micron pillar arrays are integrated into a standard CE microsystem. Since DNA molecules have to migrate in-between and interact with the pillars, pillar geometry is first demonstrated to have a direct impact on the DNA motion pattern. Electric field re-distribution is another inevitable outcome when features of sub-micron dimensions are placed inside a microchannel. This effect is verified by a numerical simulation tool. Furthermore, the integration of the closely packed sub-micron structures dramatically increases the surface to volume ratios in the microfluidic device and therefore generates a large EOF. The consequence of these additional influences implies a complexity in the measured DNA velocity and indicates that careful considerations have to be taken when these devices are used for DNA electrokinetics study or electrophoresis theory re-examination.