Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy

Yuki Suzuki, Yuji Higuchi, Kohji Hizume, Masatoshi Yokokawa, Shige H. Yoshimura, Kenichi Yoshikawa, Kunio Takeyasu

Research output: Contribution to journalArticlepeer-review

50 Citations (Scopus)

Abstract

Nucleosome is a fundamental structural unit of chromatin, and the exposure from or occlusion into chromatin of genomic DNA is closely related to the regulation of gene expression. In this study, we analyzed the molecular dynamics of poly-nucleosomal arrays in solution by fast-scanning atomic force microscopy (AFM) to obtain a visual glimpse of nucleosome dynamics on chromatin fiber at single molecule level. The influence of the high-speed scanning probe on nucleosome dynamics can be neglected since bending elastic energy of DNA molecule showed similar probability distributions at different scan rates. In the sequential images of poly-nucleosomal arrays, the sliding of the nucleosome core particle and the dissociation of histone particle were visualized. The sliding showed limited fluctuation within 50. nm along the DNA strand. The histone dissociation occurs by at least two distinct ways: a dissociation of histone octamer or sequential dissociations of tetramers. These observations help us to develop the molecular mechanisms of nucleosome dynamics and also demonstrate the ability of fast-scanning AFM for the analysis of dynamic protein-DNA interaction in sub-seconds time scale.

Original languageEnglish
Pages (from-to)682-688
Number of pages7
JournalUltramicroscopy
Volume110
Issue number6
DOIs
Publication statusPublished - 2010 May 1

Keywords

  • Atomic force microscopy
  • Chromatin
  • Fast-scanning atomic force microscopy
  • Histone
  • Nucleosome

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Instrumentation

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