Development and application of microfluidic genetic analysis systems

The work presented in this dissertation is focused on the development of instrumentation and analytical methodology for microfluidic genetic analysis systems. A fully-integrated microscale total analysis system (μ-TAS) was developed and ultimately applied to the purification, amplification, injection, and electrophoretic separation of DNA directly from sub-microliter samples of murine blood or human nasal aspirates in less than 30 min. Novel detection and flow control methods are also introduced, providing passive components that are complementary to microfluidic valves. Chapter 1 introduces generalized microfluidic and conventional concepts that are directly relevant to this work. In Chapter 2, the development of instrumentation and fabrication methods for temperature control of nanoliter-scale polymerase chain reaction (PCR) is outlined, resulting in microchip PCR in only 5 min with thermally-isolated reaction chambers. The fully-integrated work is presented in Chapter 3, with primary focus on the coupling between PCR and microchip electrophoresis (ME) using elastomeric valving technology. PCR-ME is shown to be possible in 12 min using these devices, and solid phase extraction (SPE) was then coupled to the system for SPE-PCR-ME in less than 30 min. In Chapter 4, extrinsic Fabry-Perot interferometry (EFPI) is shown to be a well-suited, versatile detection method for microfluidic systems, with the capability to measure distance, flow dynamics, refractive index, solution concentrations, and temperature in microfluidic devices---all using a robust, optical fiber-based system that is capable of multiplexing. Novel flow control concepts are then introduced in Chapter 5, based on electrical circuit analogies to fluidic networks. Fluidic rectification is shown to be possible, eliminating negative pulses in flow rate from valve-based microfluidic pumps. Additionally, the concept of discrete microfluidic capacitor components is introduced to provide frequency-dependent control over flow rates. Fluidic circuits analogous to half-wave flow rectifiers, low-pass filters, band-pass filters, AC-DC converters, and timers are shown to be possible using combinations of these passive components. Furthermore, the fundamental frequencies of fluidic band-pass filters are shifted by varying the thicknesses of capacitor membranes. This directional and frequency-dependent flow control should enhance the flexibility of microfluidic networks for various applications. Finally, future directions are outlined in Chapter 6.