Design and fabrication of PCR chip with integrated dielectrophoretic based sample pretreatment

Micro total analysis systems (µTAS) ideally integrates all steps from sample preparation to data representation of the analysis into one microfabricated system. Sample pretreatment performed on microfabricated devices is still under development and is one of the main challenges that remain in the development of true µTAS. This thesis deals with the integration of a dielectrophoretic (DEP) based sample pretreatment system with a polymerase chain reaction (PCR) microchip. The integration is achieved by development of designs that uses the photoresist SU-8 to define all the fluidic components of the two systems on glass substrates. First a PCR chip design was developed with a SU-8 based PCR chamber fabricated on a glass substrate. Integrated thin film heater and temperature sensor electrodes control the PCR thermocycling. Simulations and measurements showed that the PCR chip design was capable of fast thermocycling with heating and cooling rates in excess of 50°C/s and 30°C/s, respectively. When the PCR compatibility of the chamber surfaces was enhanced by silanization the yield of the PCR chips were up to 2/3 of the yield using conventional PCR tubes. The DEP based sample pretreatment system was based on designs with titanium and nickel silicide electrodes fabricated on various substrates with a simple SU-8 fluidic system. It was shown that DEP devices could be used to perform a number of typical sample pretreatment tasks like separation and concentration of cells. Based on the developed components an integrated device was designed and fabricated. The DEP based sample pretreatment system was connected to the PCR chamber using a fluidic system that allows the sample pretreatment to be performed in a separate medium than the PCR amplification. Initial testing of the integrated chip was performed on a sample with yeast cells and a known amount of heparin, which inhibits PCR. It was found that only the treated sample was successfully amplified. SU-8 based polymer waveguides were also developed using a fabrication process compatible with the integrated PCR chip. The waveguides had a relatively high propagation loss at wavelengths below 550nm. However, above 550nm the loss was less than 3db/cm. The functionality of the waveguides were tested in a flow cytometry setup using fluorescent beads.