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Nucleosomes in solution exist as a mixture of twist-defect states

Academic Article
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Overview

authors

  • Edayathumangalam, R. S.
  • Weyermann, P.
  • Dervan, P. B.
  • Gottesfeld, Joel
  • Luger, K.

publication date

  • January 2005

journal

  • Journal of Molecular Biology  Journal

abstract

  • The 2.0 A crystal structure of a nucleosome core particle in complex with a bivalent pyrrole-imidazole polyamide reveals that this "clamp" effectively crossbraces the two gyres of the DNA superhelix, thereby stabilizing the nucleosome against dissociation. Using X-ray crystallography and footprinting techniques, we show that the clamp preferentially binds nucleosomes over free DNA, and that nucleosomal DNA exists as a mixture of multiple twist-defect intermediates in solution. The nucleosomes exist in one of two different conformations in various crystal structures that trap twist-defect intermediates, even on a strong positioning sequence. Evidence has been obtained supporting the existence of twist-defect states in nucleosomal DNA in solution that are similar to those obtained in crystal structures. Our results also substantiate the idea that twist diffusion may represent an important means of altering the accessibility of nucleosomal DNA both in the presence and in the absence of ATP-dependent chromatin-remodelling enzymes.

subject areas

  • Animals
  • Crystallography, X-Ray
  • DNA
  • Humans
  • Imidazoles
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nucleosomes
  • Nylons
  • Pyrroles
  • Solutions
  • Xenopus laevis
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Research

keywords

  • nucleosome core particle (NCP)
  • nucleosome dynamics
  • pyrrole-imidazole polyamide (Py-Im PA) clamp
  • twist defect
  • twist diffusion
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Identity

International Standard Serial Number (ISSN)

  • 0022-2836

Digital Object Identifier (DOI)

  • 10.1016/j.jmb.2004.10.012

PubMed ID

  • 15567414
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Additional Document Info

start page

  • 103

end page

  • 114

volume

  • 345

issue

  • 1

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