Applications of Integrated Polymer Waveguides in Microsystems

Abstract

Denne PhD afhandling fokuserer på anvendelsen af integrerede polymerer bølgeledere for real-time optisk detektion i mikrofabikerede analysesystemer. Ved at anvende en ny fabrikationsteknologi til plane bølgeledere blev SU-8 bølgeledere integreret i mikrochip flow cytometer, mikrochip DEP-flow cytometer, og real-time mikrochip PCR. På grund af sine gode optiske egenskaber blev den negative epoxy fotoresist SU-8 valgt til at fremstille integreret polymer optik (bølgeledere, linser, og fiber-til-bølgeledere koblere) til optisk detektion. Det mikrofluide netværk blev også fremstillet i SU-8. Den integreret optik og det mikrofluide netværk kan derfor defineres i det samme fotolitografiske trin uden at introducerer ekstra maske trin. Disse mikro devises blev anvendt til hhv. detektion af celler, undersøgelse af celle sorterings processer, og monitering af dannelsen af PCR produkt. Derudover blev biokompatibiliteten og biokompatibiliteten af modificerede SU-8 overflader undersøgt.The research in this thesis focused on different applications of integrated polymer waveguides for real-time optical detection in µTAS (micro total analysis systems). Based on previous research efforts of our group on SU-8 waveguides,dielectrophoresis (DEP) and microchip PCR, the SU-8 waveguides were integrated into a microchip flow cytometer, a microchip DEP-flow cytometer, and a real-time microchip PCR. Those microdevices were applied for detection of cells, investigation of cell sorting processes, and monitoring of PCR products, respectively. Finally, the surface modification of SU-8 was also investigated in this thesisWith integrated polymer waveguides, a novel microchip flow cytometer was developed for the detection of cell/particle in microfluidic channels. Several different optical elements (waveguides, lens and fiber-to-waveguide couplers) were monolithically defined in same SU-8 (negative epoxy photoresist) layer with microfluidic channels using standard photolithography. Using a band-pass filter set, this microchip flow cytometer could detect three signals (forward scattering, large angle scattering and extinction) of polystyrene beads with different sizes as well as the fluorescence from two different types of labeled blood cells. Different realizations of cell-sorting microstructures combined with sample pretreatment have been developed, but most of them still use bulk optical system for monitoring purpose. Based on previously developed microchip flowcytometer, two micro flow cytometers were integrated up and downstream of a positive DEP structure for real-time monitoring of the DEP sorting process. The chips were used to quantitatively determine the influence of different factors (flow rate, applied voltage, conductivity of the sample, and frequency of the electric field) on the sorting efficiency for yeast cells. A theoretical model for the capture efficiency was developed and showed a reasonable agreement with theexperimental results. Viable and non-viable yeast cells showed different frequency dependence and were sorted with high efficiency at 2 MHz and 20 Vpp, where more than 90 % of the viable cells and less than 10 % of the non-viable cells were captured on the DEP filter. Finally, a novel real-time PCR microchip platform was developed with integratedthermal system and polymer waveguides for real-time PCR monitoring. The integrated polymer optical system was created in the SU-8 layer of the reaction chamber, without requiring any additional mask process. To realize real-time PCR, two suitable DNA binding dyes, SYTOX Orange and TO-PRO-3, were selected and added to the PCR mixture. The real-time PCR microchip was applied to detect cadF, a virulence gene of Campylobacter jejuni.Since the µTAS devices described in this thesis are all mainly constructed with SU-8. A chemical treatment method for SU-8 surface was investigated to render the biocompatibility. The biocompatibility of the treated SU-8 surface was examined by different methods (including contact angle measurements, cell culture, cell morphology, cell growth kinetics, and the whole genome expression profiles microarray analysis). The whole genome expression profile microarray analysis can provide more detailed biocompatibility information of different polymer surfaces than other methods. The results also indicated that there might be no correlation between surface hydrophobicity and biocompatibility