UC Berkeley

This dissertation demonstrates the development and application of advanced X-ray scattering techniques toward the exploration of DNA-protein interactions and engineering bionanotechnology. Herein I describe the development of size exclusion chromatography-coupled small-angle X-ray scattering with in-line multi-angle light scattering (SEC-SAXS-MALS) and X-ray scattering interferometry (XSI). SEC-SAXS-MALS is a high-throughput, multimodal structural biology approach with integrated purification whereas XSI leverages the interference pattern between ordered gold nanoparticles (AuNPs) to calculate discrete inter-AuNP distances, effectively turning them into molecular rulers. I demonstrate the application of these techniques in the study of the single-strand break (SSB) DNA-damage repair meiotic recombination 11 (MRE11) nuclease activity, poly(ADP-ribose) polymerase 1 (PARP-1) damage recognition, activation, and inhibition, and the dynamics of the DNA-dependent protein kinase holoenzyme DNA-PK complex. Additionally, I show the versatility of these techniques in bionanoengineering by exploring the surface adsorbed morphology and nanosensing mechanisms of DNA‐functionalized single‐walled carbon nanotubes (ssDNA‐SWCNTs), and the innovation of RuBisCO assemblies. Finally, I show how these techniques provide high-throughput capabilities that enable rapid disaster responses by characterizing the Nsp7, Nsp8, and Nsp12 complexes of SARS-CoV-2 involved in replication, and the exploration of rigid monoclonal antibodies to improve detection of the SARS-CoV-2 nucleocapsid.