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The Nucleosome01:19

The Nucleosome

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Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can 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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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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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 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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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
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AFM of self-assembled lambda DNA-histone networks.

YuYing Liu1, Martin Guthold2, Matthew J Snyder2

  • 1Department of Physics, College of Science, China Agricultural University, Beijing 100083, China.

Colloids and Surfaces. B, Biointerfaces
|July 5, 2015
PubMed
Summary

Atomic force microscopy revealed that DNA and histones self-assemble into polygonal networks at specific ratios. These DNA-histone networks are stable in Mg(2+) but form aggregates in Ca(2+).

Keywords:
HexagonHistoneLambda DNA (or λ-DNA)NetworkPentagonSelf-assembly

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Nanotechnology

Background:

  • DNA packaging by histone proteins is crucial for genome organization.
  • Understanding DNA-histone self-assembly is key to comprehending chromatin structure and function.
  • Atomic force microscopy (AFM) offers high-resolution imaging of biomolecular interactions.

Purpose of the Study:

  • To investigate the self-assembly behavior of lambda-DNA (λ-DNA) and histones.
  • To determine the effect of varying histone:DNA ratios on DNA organization.
  • To examine the influence of divalent cations (Mg(2+) and Ca(2+)) on DNA-histone complex structures.

Main Methods:

  • Atomic force microscopy (AFM) was employed to visualize DNA-histone structures.
  • Experiments were conducted at controlled histone:DNA ratios, ranging from none to one histone per 167 base pairs.
  • The impact of magnesium (Mg(2+)) and calcium (Ca(2+)) ions on self-assembled structures was assessed.

Main Results:

  • At low histone concentrations, individual double-stranded DNA molecules were observed.
  • Increasing histone concentrations led to the formation of extensive polygonal networks (pentagons and hexagons).
  • These networks remained stable in the presence of 20mM Mg(2+) but disassembled into aggregates in high Ca(2+).

Conclusions:

  • DNA and histones can self-assemble into stable, ordered polygonal network structures.
  • The observed networks represent potential naturally occurring DNA-histone complexes.
  • Divalent cations differentially affect the structural stability of these DNA-histone assemblies, with Ca(2+) promoting aggregation.