Reinventing the Wheel: Engineering Rolling DNA Motors with Exonuclease III for RNA-Free Autonomy and Biosensing Restricted; Files & ToC

Abstract

Synthetic DNA-based motors have emerged as powerful tools for biosensing and nanoscale actuation, with rolling motor designs offering one of the best combinations of speed, processivity, and sustained directional motion. However, these systems have primarily relied on RNA monolayers as substrate tracks, limiting their stability and applicability in complex environments. Here, we report the development of a robust, RNA-free DNA motor system powered by Exonuclease III. These motors exhibit self-avoiding rolling motion driven by enzymatic hydrolysis of a surface-bound DNA fuel strand, forming a burnt-bridge Brownian ratchet. We systematically optimized motor performance by tuning 3′ fluorophore modifications, DNA sequence composition, and surface fuel density. Fluorescence and brightfield microscopy revealed super-diffusive and Lévy-like motility under optimized conditions. Importantly, DNA-only architecture confers resistance to RNase degradation, and the system can be repurposed for motion-based biosensing via aptamer-functionalized components that selectively stall in response to viral targets. Together, this work establishes a chemically stable, tunable, and biosensing-compatible DNA motor platform suitable for directional movement across functionalized surfaces in complex biological environments.

Table of Contents

This table of contents is under embargo until 12 January 2028

About this Dissertation

Rights statement

• Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.

School	Laney Graduate School
Department	Chemistry
Degree	Ph.D.
Submission	Dissertation
Language	English
Research Field	Chemistry, Analytical Chemistry, Biochemistry
Keyword	Nuclease Synthetic motor biophysical chemistry DNA nanotechnology analytical chemistry
Committee Chair / Thesis Advisor	Khalid Salaita, Emory University
Committee Members	Laura Finzi, Clemson University Katherine Davis, Emory University

Last modified

Primary PDF

Thumbnail	Title	Date Uploaded	Actions
	File download under embargo until 12 January 2028	2025-12-08 15:54:17 -0500	File download under embargo until 12 January 2028

Supplemental Files

Thumbnail	Title	Date Uploaded	Actions