STRUCTURAL STUDIES OF NUCLEOSOMES WITH SMALL ANGLE X-RAY SCATTERING AND CONTRAST VARIATION

Tokuda, Joshua

STRUCTURAL STUDIES OF NUCLEOSOMES WITH SMALL ANGLE X-RAY SCATTERING AND CONTRAST VARIATION

Abstract

Nucleosomes are the fundamental units of DNA packaging and play central roles in regulating genetic activity in eukaryotic cells. High-resolution crystal structures deliver detailed snapshots of the nucleosome in its most stable conformations. However, nucleosomes are dynamic structures that populate diverse conformations as they regulate DNA accessibility. A full understanding of how DNA is processed requires knowledge of these conformations and the interplay of factors that coordinate their formation. In this dissertation, we describe a new approach using small angle x-ray scattering to resolve alternate nucleosome conformations and investigate the mechanisms that facilitate their formation. We begin by studying the salt-induced disassembly pathway of nucleosomes. By modulating the ionic strength of the solution, we globally destabilize nucleosome structures and identify key intermediates that reflect the intrinsic mechanical propensities of the nucleosome. We then investigate how the chromatin remodeler, Chd1, reorganizes nucleosome structure in a nucleotide-dependent manner. Our results suggest that the biophysical properties of the DNA play important roles in directing how alternate conformations are formed.

Date Issued

2017-08-30

Keywords

contrast variation; nucleosomes; SAXS; small angle x-ray scattering; time resolved; Biophysics

Committee Chair

Pollack, Lois

Committee Member

Zipfel, Warren R.
Crane, Brian

Degree Discipline

Biophysics

Degree Name

Ph. D., Biophysics

Degree Level

Doctor of Philosophy

Rights

Attribution-ShareAlike 2.0 Generic

Rights URI

https://creativecommons.org/licenses/by-sa/2.0/

Types

dissertation or thesis