Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles.

Autor:	Mauney AW; School of Applied and Engineering Physics, Cornell University, Ithaca, New York., Tokuda JM; School of Applied and Engineering Physics, Cornell University, Ithaca, New York., Gloss LM; School of Molecular Biosciences, Washington State University, Pullman, Washington., Gonzalez O; Department of Mathematics, University of Texas, Austin, Texas., Pollack L; School of Applied and Engineering Physics, Cornell University, Ithaca, New York. Electronic address: lp26@cornell.edu.
Jazyk:	angličtina
Zdroj:	Biophysical journal [Biophys J] 2018 Sep 04; Vol. 115 (5), pp. 773-781. Date of Electronic Publication: 2018 Jul 31.
DOI:	10.1016/j.bpj.2018.07.009
Abstrakt:	DNA is tightly wrapped around histone proteins in nucleosome core particles (NCPs) yet must become accessible for processing in the cell. This accessibility, a key component of transcription regulation, is influenced by the properties of both the histone proteins and the DNA itself. Small angle x-ray scattering with contrast variation is used to examine how sequence variations affect DNA unwrapping from NCPs at different salt concentrations. Salt destabilizes NCPs, populating multiple unwrapped states as many possible unwrapping pathways are explored by the complexes. We apply coarse-grained Monte Carlo methods to generate realistic sequence-dependent unwrapped structures for the nucleosomal DNA with thermal variations. An ensemble optimization method is employed to determine the composition of the overall ensemble as electrostatic interactions are weakened. Interesting DNA-sequence-dependent differences are revealed in the unwrapping paths and equilibrium constants. These differences are correlated with specific features within the nucleic acid sequences. (Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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