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DNA-dependent divalent cation binding in the nucleosome core particle.

Curt A Davey1, Timothy J Richmond

  • 1Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, CH-8093 Zürich, Switzerland.

Proceedings of the National Academy of Sciences of the United States of America
|August 10, 2002
PubMed
Summary

Divalent cations like manganese (Mn2+) bind specifically to nucleosomal DNA's major groove. This sequence-specific binding influences DNA structure and interactions within the nucleosome core particle.

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Area of Science:

  • Structural biology
  • Molecular genetics
  • Biochemistry

Background:

  • Divalent cations can affect nucleosome structure and function.
  • Understanding cation-nucleic acid interactions is crucial for molecular biology.

Purpose of the Study:

  • To characterize the binding of manganese ions (Mn2+) to nucleosomal DNA.
  • To define the specificity and mode of divalent cation interaction with DNA in a nucleosome core particle.

Main Methods:

  • X-ray crystallography at 1.9-Å resolution.
  • Analysis of the nucleosome core particle structure.

Main Results:

  • Manganese ions bind with high occupancy to the major groove of specific DNA sequences (GG and GC steps).

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  • Binding sites are dictated by sequence context and the DNA's orientation within the nucleosome.
  • Conformational differences between dinucleotide sites explain the specificity of metal binding.

    • Conclusions:

    • Mn2+ exhibits sequence-specific binding to nucleosomal DNA, primarily in the major groove.
    • This specific binding is influenced by local DNA conformation and sequence context.
    • Cation binding may play a role in modulating nucleosome positioning and interactions with nuclear factors.