CONFORMATIONAL DYNAMICS OF DNA AND PROTEIN-DNA COMPLEXES AT SINGLE-STRANDED-DOUBLE-STRANDED DNA JUNCTIONS
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Date
2024-03-25
Authors
Maurer, Jack
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Publisher
University of Oregon
Abstract
Most biological systems, particularly protein-DNA complexes, leverage a dynamic evolution of their structure to perform a myriad of functions within the context of the cell. Decades of detailed biophysical research have established that the intricacies of such systems stem heavily from their dynamic evolution, abandoning the previous notion of a purely static ‘structure-function’ relationship. This dissertation introduces a new polarization-sensitive methodology for studying the dynamic evolution of local conformation in single-molecules of dsDNA containing an i(Cy3)2 dimer. The methodology developed during this dissertation is applied to DNA under a variety of experimental conditions as well as protein-DNA complexes. A massively parallel computational pipeline was developed in the course of this work to aid the optimization of kinetic network models, which forms the basis for all current analyses of single-molecule data in the Marcus and von Hippel lab. The primary discovery of this work is the persistence of four relevant conformational macrostates in DNA only systems and five relevant conformational macrostates in the protein-DNA systems examined. The thermodynamic and mechanical stability of these systems is analyzed in detail and structural mechanisms are proposed to merge the observed dynamics with hypothesized local conformations during the dynamic evolution of these ubiquitous biological systems.
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Keywords
DNA, Kinetics, Macromolecular dynamics, protein-DNA interactions, single molecule, spectroscopy