Journal article
DNA shape dominates sequence affinity in nucleosome formation
Physical review letters, v 113(16), pp 168101-168101
17 Oct 2014
PMID: 25361282
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA's histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA's intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.
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Details
- Title
- DNA shape dominates sequence affinity in nucleosome formation
- Creators
- Gordon S Freeman - University of Wisconsin–MadisonJoshua P Lequieu - University of ChicagoDaniel M Hinckley - University of Wisconsin–MadisonJonathan K Whitmer - University of Wisconsin–MadisonJuan J de Pablo - University of Chicago
- Publication Details
- Physical review letters, v 113(16), pp 168101-168101
- Publisher
- Cold Spring Harbor Press
- Grant note
- T32HC002760 / NHLBI NIH HHS
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000344032500010
- Scopus ID
- 2-s2.0-84908042690
- Other Identifier
- 991020950676304721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Physics, Multidisciplinary