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A simple probe for DNA accessibility in chromatin

P Clark1, G L Eichhorn

  • 1National Institutes of Health, National Institute on Aging, Gerontology Research Center, Laboratory of Cellular and Molecular Biology, Baltimore, Maryland 21224, USA.

Journal of Inorganic Biochemistry
|September 1, 1995
PubMed
Summary
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Copper(II) ions destabilize DNA, lowering its melting temperature. However, this effect is blocked by histone H-1 in chromatin, suggesting histone H-1 binding protects DNA structure.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • DNA's double helix structure is maintained by hydrogen bonds between base pairs.
  • Chromatin is a complex of DNA and proteins (histones) that packages DNA in eukaryotic cells.
  • Histone H-1 plays a role in chromatin condensation and DNA accessibility.

Purpose of the Study:

  • To investigate the effect of Copper(II) ions on DNA and chromatin stability.
  • To determine the role of histone H-1 in mediating DNA accessibility within chromatin.
  • To explore the potential of using Cu(II) as a probe for chromatin structural changes.

Main Methods:

  • Treatment of purified DNA and soluble chromatin with Cu(II) ions.
  • Heating treated samples to determine melting temperature (Tm).

Related Experiment Videos

  • Removal of histone H-1 via affinity chromatography.
  • Modification of histone H-1 via mild acetylation and reaction with divalent metal ions.

    • Main Results:

    • Cu(II) treatment significantly decreased the Tm of purified DNA.
    • Cu(II) treatment did not affect the Tm of intact chromatin, indicating blocked DNA accessibility.
    • Removal or reduced affinity of histone H-1 to DNA restored Cu(II)-induced Tm lowering.
    • Acetylation of histone H-1 or reaction with Mg(II), Mn(II), or Co(II) also increased DNA accessibility to Cu(II).

    Conclusions:

    • Histone H-1 binding to DNA sterically hinders Cu(II) access, protecting the DNA double helix.
    • Changes in histone H-1 affinity or accessibility directly correlate with DNA's susceptibility to destabilization.
    • This Cu(II)-based assay offers a simple method to qualitatively assess chromatin structural alterations related to DNA-histone interactions.