NOVEL MODELING METHODS FOR STUDYING NUCLEOSOMES WITH CONTRAST VARIATION SMALL ANGLE X-RAY SCATTERING

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Abstract
DNA in cells must be packaged for compaction and organization. Nucleosomes are the fundamental unit of this packaging and play a central role in regulating access to the genome. Higher order structuring of the genome is then done by manipulating the interactions between nucleosomes. The interactions between the protein and DNA are highly dynamic and are important for understanding the accessibility of genomic DNA. Small angle x-ray scattering (SAXS) is an ideal method for studying these dynamics due to the high scattering of DNA but requires detailed models of the system of interest to interpret the data. In this dissertation we describe a new method to model the dynamics of nucleosomes and nucleosome arrays for SAXS and its application to a variety of nucleosomal systems. We begin with an investigation of how DNA sequence modulates the unwrapping of nucleosomes undergoing salt destabilization. We observe that sequence motifs correlate with the unwrapping pathways and can cause asymmetry in the unwrapping. Next, we study the impact of histone variant H2A.Z substitution. We find that H2A.Z causes complex-wide changes in binding through allosteric effects and observe a stable unwrapping intermediate. Finally, we expand the method to arrays of nucleosomes to understand the structure of trinucleosomes in solution. By analyzing the relative distances and orientations of the individual nucleosomes we conclude that two well separated populations exist. Overall, this new method allows for large pools of nucleosomal structures to be generated quickly, which have proven to be invaluable to understanding SAXS experiments.
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197 pages
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2020-08
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Pollack, Lois
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Wang, Jane
Wang, Michelle D.
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Physics
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Ph. D., Physics
Degree Level
Doctor of Philosophy
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dissertation or thesis
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