Date of Award

12-2017

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Mechanical Engineering

Committee Chair

Jong Hyun Choi

Committee Member 1

Chengde Mao

Committee Member 2

Andrew Mugler

Committee Member 3

Cagri A. Savran

Abstract

A dynamic DNA nanosystem exploits the programmable structure and energy landscape of DNA self-assembly to encode designed processes in a fuctuating molecular environment. One type of such a dynamic system, DNA walker, is reminiscent of biological motor proteins that convert chemical energy into mechanical translocation. Typical DNA walker travels tens of nanometers at a speed orders of magnitude slower than motor proteins. Two major challenges limited the development of functional DNA walkers. First, there are no suitable characterization methods that o˙er adequate spatial and temporal resolution to extract walker kinetics. Second, no guidelines have been established for the design and development of DNA walkers with specifed properties. In this work, an enzymatic DNA walker system that integrate oligonucleotides with nanomaterials is designed. This approach takes advantage of novel optical properties of nanomaterials and sub-di˙raction imaging techniques to study the kinetics and biophysical nature of synthetic DNA walkers. Design principles are extracted from walker kinetics for constructing functional walkers that can rival motor proteins. Multiple schemes are explored to regulate the walker motility so that various behaviors can be encoded into the system. This work demonstrates novel methods to design and construct molecular systems with programmed functions, which will pave the road for creating synthetic systems with encoded behaviors from the bottom up.

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