DNA Origami Assembly Dynamics, Directed Surface Placement, and PNA-Based Detection of RNA Editing Events Open Access

Abstract

Nucleic acids are uniquely suited as programmable materials because of their predictable base-pairing interactions, enabling the self-assembly of structures ranging from simple duplexes to complex hierarchical nanostructures. This programmability has driven significant advances in nanotechnology and biotechnology by providing a versatile platform for engineering functional materials for applications in molecular diagnostics, therapeutics, and nanoscale fabrication. In parallel, the ability to precisely organize materials at the nanoscale offers new opportunities for next-generation electronic devices, photonic materials, and bottom-up manufacturing strategies that complement conventional lithographic techniques.

This dissertation explores the design and application of programmable nucleic acid systems across multiple areas of DNA nanotechnology. First, fluorogenic peptide nucleic acid (PNA) probes were developed for the selective detection of adenosine-to-inosine (A-to-I) RNA editing, providing a platform for sequence-specific nucleic acid sensing. Second, competitive assembly and transformation studies of DNA origami helix bundles were performed to investigate the hierarchical assembly pathways and structural reconfiguration of DNA nanostructures, providing new insights into the mechanisms governing DNA origami assembly. Finally, the directed placement of DNA origami on lithographically patterned inorganic substrates was investigated as a foundation for the controlled growth of three-dimensional DNA nanocrystal architectures.

In addition to these experimental studies, this dissertation reviews the emerging potential of DNA nanotechnology for therapeutic drug delivery and mechanotransduction studies, highlighting future opportunities for programmable nucleic acid materials in medicine and bioengineering. Collectively, these studies advance the understanding of programmable nucleic acid self-assembly while demonstrating strategies for integrating DNA nanotechnology with molecular sensing and nanoscale fabrication, thereby contributing to the continued development of functional nucleic acid materials for biomedical and nanofabrication applications.

Table of Contents

Introduction........................................................................................................................................................................... 1

1.1. Nucleic Acids as Programmable Materials..................................................................................................................... 1

1.2 Peptide Nucleic Acids (PNA)...........................................................................................................................................2

1.3 RNA Editing and Biological Significance......................................................................................................................... 4

1.4DNA Nanotechnology .....................................................................................................................................................7

1.5 DNA Origami Technology............................................................................................................................................... 9

Applications of DNA Origami..............................................................................................................................................11

Drug Delivery.....................................................................................................................................................................11 

Biosensingy.......................................................................................................................................................................12  

Nanofabrication and Nanoelectronics..................................................................................................................................12

Molecular Robotics.............................................................................................................................................................13

1.6 Surface Patterning and Placement of DNA Origami...........................................................................................................13

1.7 Understanding DNA Origami Assembly Pathways..............................................................................................................15

1.8 Dissertation Objectives....................................................................................................................................................16

2 Detection of Adenosine-to-Inosine Editing Sites in RNA Using an Intercalating Triplex PNA Probe..........................................20

2.1 Introduction....................................................................................................................................................................20

2.2 Design of an Intercalating Triplex PNA Probe.....................................................................................................................21

2.3 Materials and Methods.....................................................................................................................................................23

2.4 Results and Discussion.....................................................................................................................................................27

2.5 Conclusion......................................................................................................................................................................30

3. DNA Origami Crystal Assembly on Electron-Beam Lithography (EBL) Wafers..........................................................................32

3.1Introduction.......................................................................................................................................................................32

3.2 DNA Origami Placement Strategy........................................................................................................................................34

3.3Materials and Methods........................................................................................................................................................36

3.4 Fabrication and Placement Results...................................................................................................................................... 41

3.5Conclusions and Future Directions.......................................................................................................................................44

4.Mechanistic Investigation of DNA Origami Assembly Through Competitive Assembly and Transformation Assays.......................46

4.1 Introduction.......................................................................................................................................................................46

4.2 9, 15 and 45 Helix Bundle competitive and reconfiguration competitive assembly design..........................................................48

4.3 Materials and Methods ........................................................................................................................................................54

4.4 Results and Discussion.........................................................................................................................................................55

4.5 Conclusions and Future Directions........................................................................................................................................60

5 Conclusions and Future Directions...........................................................................................................................................62

 

 

 

About this Dissertation

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School	Laney Graduate School
Department	Chemistry
Degree	Ph.D.
Submission	Dissertation
Language	English
Research Field	Chemistry, General
Keyword	Nucleic Acid Technology DNA Nanotechnology Peptide Nucleic Acids RNA Editing DNA origami
Committee Chair / Thesis Advisor	Yonggang Ke, Emory University
Committee Members	Monika Raj, Emory University Vincent Conticello, Emory University

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	Supplemental Information (The following appendix contains supplemental characterization data supporting the work presented in Chapters 2–4, including ^1H NMR spectra, mass spectra, HPLC chromatograms, UV melting (Tm) analyses, and additional DNA origami design information. These data provide experimental validation of synthesized PNA monomers, FIT-PNA probes, and DNA origami structures described throughout this dissertation.)	2026-08-06 16:46:58 -0400	Press to Select an action Download