Design and Study of Hybrid DNA Nanostructures and Complex 3D DNA Materials

Over the past four decades, DNA nanotechnology has grown exponentially from a field focused on simple structures to one capable of synthesizing complex nano-machines capable of drug delivery, nano-robotics, digital data storage, logic gated circuitry, nano-photonics, and other applications. The construction of these nanostructures is possible because of the predictable and programmable Watson-Crick base pairing of DNA. However, there is an increasing need for the incorporation of chemical diversity and functionality into these nanostructures. To overcome this challenge, this work explored creating hybrid DNA nanostructures by making self-assembling small molecule/protein-DNA conjugates.In one direction, well studied host-guest interactions (i.e. cucurbituril[7]-adamantane) were used as the choice of self-assembling species. Binding studies using these small molecule-DNA conjugates were performed and thereafter they were used to assemble larger DNA origami nanostructures. Finally, a stimulus responsive DNA nano-box that opens and closes based on these interactions was also demonstrated. In another direction, a trimeric KDPG aldolase protein-DNA conjugate was probed as a structural building block by assembling it into a DNA origami tetrahedron with four cavities. This hybrid building block was thereafter characterized by single particle cryo-EM and the resulting electron density map was best fit by simulating origami cages with varying number of proteins (ranging from 0 to 4). Next, to increase access and for larger democratization of the field, an automation designer software tool capable of making DNA nanostructures was made. In this work, the focus was on making curved 3D DNA nanostructures. The last direction probed in this work was to make optical metamaterials based on complex 3D DNA architectures. Realization of a self-assembled 3D tetrastack geometry is still an unachieved dream in the field of DNA self-assembly. Thus, this direction was probed using DNA origami icosahedrons. Finally, the work covered in my thesis probes multiple directions for advancing DNA nanotechnology, both fundamentally and for potential applications.