Dissertation/Thesis Abstract

Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering
by Howell, Steven C., Ph.D., The George Washington University, 2016, 220; 3738561
Abstract (Summary)

Chromatin conformation and dynamics remains unsolved despite the critical role of the chromatin in fundamental genetic functions such as transcription, replication, and repair. At the molecular level, chromatin can be viewed as a linear array of nucleosomes, each consisting of 147 base pairs (bp) of double-stranded DNA (dsDNA) wrapped around a protein core and connected by 10 to 90 bp of linker dsDNA.

Using small-angle X-ray scattering (SAXS), we investigated how the conformations of model nucleosome arrays in solution are modulated by ionic condition as well as the effect of linker histone proteins. To facilitate ensemble modeling of these SAXS measurements, we developed a simulation method that treats coarse-grained DNA as a Markov chain, then explores possible DNA conformations using Metropolis Monte Carlo (MC) sampling. This algorithm extends the functionality of SASSIE, a program used to model intrinsically disordered biological molecules, adding to the previous methods for simulating protein, carbohydrates, and single-stranded DNA. Our SAXS measurements of various nucleosome arrays together with the MC generated models provide valuable solution structure information identifying specific differences from the structure of crystallized arrays.

Indexing (document details)
Advisor: Qiu, Xiangyun
Commitee: Curtis, Joseph E., Krueger, Susan, Peng, Weiqun, Reeves, Mark
School: The George Washington University
Department: Physics
School Location: United States -- District of Columbia
Source: DAI-B 77/04(E), Dissertation Abstracts International
Source Type: DISSERTATION
Subjects: Physics, Biophysics
Keywords: Chromatin, DNA, Monte Carlo, Nucleosome, Saxs, Simulation
Publication Number: 3738561
ISBN: 9781339290249
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