Probing the structure and dynamics of nucleosomes using atomic force microscopy imaging

Micah P. Stumme-Diers, Tommy Stormberg, Zhiqiang Sun, Yuri L. Lyubchenko

Research output: Contribution to journalArticle

Abstract

Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription to take place in eukaryotic cells. The dynamics of nucleosomes provides access to the DNA by replication and transcription machineries, and critically contributes to the molecular mechanisms underlying chromatin functions. Single-molecule studies such as atomic force microscopy (AFM) imaging have contributed significantly to our current understanding of the role of nucleosome structure and dynamics. The current protocol describes the steps enabling high-resolution AFM imaging techniques to study the structural and dynamic properties of nucleosomes. The protocol is illustrated by AFM data obtained for the centromere nucleosomes in which H3 histone is replaced with its counterpart centromere protein A (CENP-A). The protocol starts with the assembly of mono-nucleosomes using a continuous dilution method. The preparation of the mica substrate functionalized with aminopropyl silatrane (APS-mica) that is used for the nucleosome imaging is critical for the AFM visualization of nucleosomes described and the procedure to prepare the substrate is provided. Nucleosomes deposited on the APS-mica surface are first imaged using static AFM, which captures a snapshot of the nucleosome population. From analyses of these images, such parameters as the size of DNA wrapped around the nucleosomes can be measured and this process is also detailed. The time-lapse AFM imaging procedure in the liquid is described for the high-speed time-lapse AFM that can capture several frames of nucleosome dynamics per second. Finally, the analysis of nucleosome dynamics enabling the quantitative characterization of the dynamic processes is described and illustrated.

Original languageEnglish (US)
Article numbere58820
JournalJournal of Visualized Experiments
Volume2019
Issue number143
DOIs
StatePublished - Jan 2019

Fingerprint

Nucleosomes
Atomic Force Microscopy
Atomic force microscopy
Imaging techniques
Mica
DNA
Transcription
DNA Replication
Substrates
Chromatin
Dilution
Dynamical systems
Visualization
Proteins
Centromere
Molecules
Eukaryotic Cells
Liquids
Histones

Keywords

  • AFM
  • Biochemistry
  • Chromatin
  • DNA
  • Dynamics
  • Epigenetics
  • Histones
  • Imaging
  • Issue 143
  • Nucleosome
  • Single - molecule
  • Structure
  • Time-lapse

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Probing the structure and dynamics of nucleosomes using atomic force microscopy imaging. / Stumme-Diers, Micah P.; Stormberg, Tommy; Sun, Zhiqiang; Lyubchenko, Yuri L.

In: Journal of Visualized Experiments, Vol. 2019, No. 143, e58820, 01.2019.

Research output: Contribution to journalArticle

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