A Markov model for the dynamics of the nucleosome

We study the dynamics of the nucleosome, the most abundant DNA protein complex in eukaryotic cells. The dynamics consist of two mechanisms, site exposure and sliding, which are crucial for making DNA accessible to DNA-binding proteins. The intertwining of both effects leads to a rich stochastic proc...

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Bibliographic Details
Published in:Journal of physics. A, Mathematical and theoretical Mathematical and theoretical, 2013-03, Vol.46 (9), p.1-15
Main Authors: van Opheusden, B, Redig, F, Schiessel, H
Format: Article
Language:English
Subjects:
Accessibility
Constants
Deoxyribonucleic acid
Dynamic tests
Dynamics
Exposure
Proteins
Sliding
Stochastic processes
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Summary:We study the dynamics of the nucleosome, the most abundant DNA protein complex in eukaryotic cells. The dynamics consist of two mechanisms, site exposure and sliding, which are crucial for making DNA accessible to DNA-binding proteins. The intertwining of both effects leads to a rich stochastic process that has not been studied before. Within the assumptions of our model, nucleosomes perform a symmetric random walk along the DNA strand. We investigate how the diffusion constant depends on the relative rates of site exposure and sliding.
ISSN:1751-8113
1751-8121
DOI:10.1088/1751-8113/46/9/0950051