CONFORMATIONAL DYNAMICS OF DNA AND PROTEIN-DNA COMPLEXES AT SINGLE-STRANDED-DOUBLE-STRANDED DNA JUNCTIONS

Simple item page
dc.contributor.advisorMarcus, Andrew
dc.contributor.authorMaurer, Jack
dc.date.accessioned2024-03-25T17:38:11Z
dc.date.available2024-03-25T17:38:11Z
dc.date.issued2024-03-25
dc.description.abstractMost 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.en_US
dc.identifier.urihttps://hdl.handle.net/1794/29293
dc.language.isoen_US
dc.publisherUniversity of Oregon
dc.rightsAll Rights Reserved.
dc.subjectDNAen_US
dc.subjectKineticsen_US
dc.subjectMacromolecular dynamicsen_US
dc.subjectprotein-DNA interactionsen_US
dc.subjectsingle moleculeen_US
dc.subjectspectroscopyen_US
dc.titleCONFORMATIONAL DYNAMICS OF DNA AND PROTEIN-DNA COMPLEXES AT SINGLE-STRANDED-DOUBLE-STRANDED DNA JUNCTIONS
dc.typeElectronic Thesis or Dissertation
thesis.degree.disciplineDepartment of Chemistry and Biochemistry
thesis.degree.grantorUniversity of Oregon
thesis.degree.leveldoctoral
thesis.degree.namePh.D.

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Maurer_oregon_0171A_13764.pdf
Size:
9.58 MB
Format:
Adobe Portable Document Format
Download

Collections

Theses and Dissertations
Chemistry Theses and Dissertations