Purdue University Graduate School
Paluzzi Dissertation final.pdf (3.52 MB)


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posted on 2023-11-17, 20:16 authored by Victoria Elizabeth PaluzziVictoria Elizabeth Paluzzi

DNA sequence design requires the ability to identify possible tertiary structural defects, secondary structure disruptions, and self-complimentary stretches that will disallow your complimentary strands to come together to form the desired duplex design. However, there is a need for those self-complimentary stretches, especially when designed with the intent for this to homo-oligomerize into the desired building block. With the programmability of nucleic acid hybridization, there is an expanding field wherein this specific, self-complimentary design feature can give new possibility of fine-tuning DNA self-assembly (Chapter 1) or overcome a previously thought limit of DNA ligation (Chapter 2).

The first chapter will closely look at the branched kissing loop interaction. This interaction was studied as a homo-polymerizable DNA building block that is topologically closed. As such, this paranemic motif has increased stability due to the Watson-Crick base pairing being “protected” by a 3-base adenine branch which close the loop of the sticky-end, meaning no free ends in the binding region. With this, herein we report that the intended higher-level structure could influence the lower-level building block formation. In DNA nanotechnology, this could mean the final higher-level structure would allow for fine-tuning as this would dictate the building blocks that fill in the defected parts of the higher-level structure.

The second chapter looks at the more finite than broad picture. Whilst the first chapter focusses on the impact the microscale has on the nanoscale through a homo-polymerizable design, the second chapter focusses on the ability to break barriers with homo-polymerizable design. In this chapter, we prove that with our splint strand design, when improved with a hairpin loop on the terminal ends, we can ligate DNA strands enzymatically as short as 16 nucleotides with an efficiency of 97% at high concentrations (100 uM). These hairpins allow for a stable, robust splint strand as they are a self-complimentary region which will maintain its shape throughout the process of joining together the 5’ and 3’ ends of the target strand.

Overall, this dissertation hopes to prove that homo-polymerizable DNA sequence designs are helping expand upon the DNA nanotechnology toolbox by introducing new possibilities for nanoscale design, as well as push past previously held boundaries through necessary added stability afforded by the self-complimentary strands.


Experimental and Computational Studies of Ligated 3D DNA Crystals

Directorate for Engineering

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Collaborative Research: FTE: Medium: Three Dimensional Algorithmic Assembly and Information Storage

Directorate for Computer & Information Science & Engineering

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Degree Type

  • Doctor of Philosophy


  • Chemistry

Campus location

  • West Lafayette

Advisor/Supervisor/Committee Chair

Chengde Mao

Additional Committee Member 2

Jong H. Choi

Additional Committee Member 3

Elizabeth I. Parkinson

Additional Committee Member 4

Scott A. McLuckey