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Related Concept Videos

The Nucleosome Core Particle02:10

The Nucleosome Core Particle

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Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
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Related Experiment Video

Updated: Apr 18, 2026

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

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Multiscale modelling of nucleosome core particle aggregation.

Alexander P Lyubartsev1, Nikolay Korolev, Yanping Fan

  • 1Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden.

Journal of Physics. Condensed Matter : an Institute of Physics Journal
|January 8, 2015
PubMed
Summary

Multivalent cations drive nucleosome core particle (NCP) self-assembly into stacked columnar phases. Coarse-grained simulations reveal how these NCP interactions lead to cluster formation, mimicking in vivo chromatin structures.

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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
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Area of Science:

  • Biophysics
  • Computational Biology
  • Materials Science

Background:

  • Nucleosome core particles (NCPs) are fundamental to chromatin structure.
  • NCPs exhibit phase behavior and stacking in the presence of multivalent cations.
  • Understanding NCP self-assembly mechanisms is crucial for chromatin research.

Purpose of the Study:

  • To model the interactions and self-assembly of NCP solutions induced by multivalent cations.
  • To develop a multiscale coarse-grained (CG) simulation approach for NCPs.
  • To investigate the role of cobalt(III)hexammine (CoHex(3+)) in NCP self-assembly.

Main Methods:

  • Developed an advanced CG NCP model.
  • Employed continuum simulations with explicit CoHex(3+) counterions.
  • Utilized the inverse Monte Carlo method to derive effective interaction potentials for a 'super-CG' NCP model.
  • Performed large-scale simulations of up to 5000 NCPs.

Main Results:

  • The 'super-CG' NCP model successfully simulated self-assembly induced by CoHex(3+).
  • Simulated systems formed large clusters of stacked NCPs.
  • Observed lack of long-range order in simulated clusters, consistent with experimental data.

Conclusions:

  • The multiscale CG simulation approach effectively models NCP self-assembly.
  • Multivalent cations play a critical role in inducing NCP stacking and cluster formation.
  • The findings provide insights into chromatin organization principles.