2025 Theses Doctoral

Functional DNA Nano-architectures with Chiroptical, Catalytic, and Thermally Responsive Properties

Shen, Jundai

DNA self-assembly provides a versatile platform for organizing hybrid functional materials whose properties emerge from encoded geometry, altered microenvironment, and chemical modifications. This dissertation explores how coupling DNA nanoarchitectures with inorganic nanoparticles, enzymes, and stimuli-responsive biomolecules alters and regulates optical, catalytic, and thermally responsive behaviors.

The first part of this work (Chapter 2) discusses the usage of DNA origami as a modular building block for functional integration and multidimensional architecture assemblies. I illustrated the general methodology to construct DNA origami that integrates hybrid nanomaterials with engineered ssDNA extensions. I also explored the construction of multidimensional origami assemblies using color-coded hybridization schemes. Building on this structural control, the dissertation next investigates how integrating different classes of nanomaterials with DNA origami scaffolds can generate emergent functions.

First, I examined the formation and optical response of chiral plasmonic architectures created by positioning gold nanoparticles at prescribed vertices of DNA origami cubes (Chapter 3). This system demonstrates how precise three-dimensional spatial arrangement and symmetry breaking translate into measurable chiroptical behavior via single-particle dark-field CD scattering. Next, this dissertation (Chapter 4) explores DNA origami as an enzymatic scaffold for modulating biocatalytic behavior. By anchoring single enzymes at prescribed positions within octahedral, cubic, and tetrahedral DNA frameworks, this work demonstrates how nanoscale geometry, spatial confinement, local electrostatics, and anchoring orientation shape catalytic parameters. In parallel, multienzyme cascades were examined within a voxel-encoded DNA lattice to investigate how hierarchical organization and DNA-mediated microenvironments alter cascade efficiency.

The final component of this thesis (Chapter 5) introduces hybrid DNA-ELP (elastin-like-polypeptides)-AuNPs that integrate the contrasting thermal behaviors of DNA melting and ELP coacervation. By conjugating AuNPs with both DNA linkers and ELP–DNA linkers, I demonstrate that the system can undergo non-monotonic, re-entrant thermal assembly transitions.