Identifier

etd-12102012-072732

Degree

Doctor of Philosophy (PhD)

Department

Mechanical Engineering

Document Type

Dissertation

Abstract

The growing needs for cheaper and faster sequencing of long biopolymers such as DNA and RNA have prompted the development of new technologies. Among the novel techniques for analyzing these biopolymers, an approach using nanochannel based fluidic devices is attractive because it is a label-free, amplification-free, single-molecule method that can be scaled for high-throughput analysis. Despite recent demonstrations of nanochannel based fluidic devices for analyzing physical properties of such biopolymers, most of the devices have been fabricated in inorganic materials such as silicon, silicon nitride and glass using expensive high end nanofabrication techniques such as focused ion beam and electron beam lithography. In order to use the nanochannel based fluidic devices for a variety of bioanalyses, it is imperative to develop a technology for low cost and high through fabrication of such devices and demonstrate the feasibility of the fabricated nanochannel based fluidic devices in obtaining information on biopolymers. We developed a low cost and high throughput method to build polymer-based nanofluidic devices with sub-100 nm nanochannels using direct imprinting into polymer substrates. Imprinting with the polymer stamps showed good replication fidelity for multiple replication processes, preventing damage of the expensive nanopatterned master and reducing undesirable deformation in the molded polymer substrate. This approach opened up a possibility to build cheap and disposable polymer nanofluidic devices for single molecule analysis. The ion transportation and DNA motion in nanofluidic systems were studied. Simulation and experiment results indicate that fast degeneration of the electric field at micro/nano interface plays a major role, in addition to the bulk flow in the microfluidic networks. Inlet structures and bypass microchannels were designed and built, the use of which has proven to enable enhancing the DNA capture rate by over 500 %. Attributed to the improved capture rate, the blockade current of DNA translocation though a nanochannel was also measured. We observed in the current versus time curves both current increase and decrease in the existence of a DNA molecule in the nanochannel, which we attributed to the ion channel blockage and electrical double layer formed around the DNA molecule, respectively.

Date

2013

Document Availability at the Time of Submission

Release the entire work immediately for access worldwide.

Committee Chair

Park, Sunggook

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