Degree

Doctor of Philosophy (PhD)

Department

Mechanical Engineering

Document Type

Dissertation

Abstract

Mechanically robust solid-state nanopores have the potential to be the next generation DNA sensing platforms. However, mass production and limited base-calling accuracy are the hurdles for solid-state nanopore based DNA sensing. In order to solve these problems, a polymer dual-nanopore device fabricated via high throughput nanoimprint lithography (NIL) was proposed to sequence DNA by time-of-flight (ToF) measurement. As a proof of concept, this study presents mononucleotides discrimination via ToF measurement using polymer in-plane dual-nanopore device.

First, fabrication of polymer in-plane nanopore with controllable dimensions was studied in consideration of experimental conditions and materials selection. Then, surface charge density effect on DNA translocation through in-plane nanopore was studied numerically and experimentally using fabricated nanopore devices on PEGDA, PMMA and COC. λ-DNA sensing was only observed in PEGDA device with a surface charge density lower than the threshold surface charge density predicted by COMSOL simulation.

With demonstrated single molecule sensing ability, mononucleotides were introduced to PEGDA dual-nanopore with 500 nm flight tube and discriminated under various conditions. At pH 8.0, mononucleotides were driven by eletrophoretic motion and their ToF was in a decreasing order of dGMP > dAMP > dCMP > dTMP. At pH 10.0, mononucleotides were driven by electroosmotic flow (EOF) due to a higher surface charge density on nanochannel walls and ToF was in the same order as pH 8.0 with an average identification accuracy of 55%. Dual-nanopore device with 1 μm flight tube was then used to improve the average identification accuracy to 75%. Finally, dGMP and dTMP in a mix solution were dicriminated by their ToF difference.

Date

10-24-2018

Committee Chair

Park, Sunggook

Available for download on Thursday, October 24, 2019

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