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Related Experiment Videos

Effect of force on mononucleosomal dynamics.

Shirley Mihardja1, Andrew J Spakowitz, Yongli Zhang

  • 1Department of Chemistry, University of California, Berkeley, CA 94720, USA.

Proceedings of the National Academy of Sciences of the United States of America
|October 18, 2006
PubMed
Summary

We studied how nucleosomes unravel using single-molecule optical trapping. The outer DNA wrap reversibly opens and closes, while the inner wrap

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Structural Biology

Background:

  • Nucleosomes are fundamental units of DNA packaging in eukaryotes.
  • Understanding nucleosome dynamics is crucial for gene regulation and DNA-related processes.
  • The mechanical properties of nucleosomes are key to their function.

Purpose of the Study:

  • To investigate the force-induced unraveling of single nucleosome core particles.
  • To characterize the mechanical behavior and energetics of nucleosome unwrapping.
  • To understand the distinct stages of nucleosome unraveling and their environmental sensitivity.

Main Methods:

  • Utilized single-molecule optical-trapping techniques.
  • Employed DNA constructs with the 601 nucleosome-positioning sequence.

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  • Analyzed force-dependent equilibrium constants and un/wrapping rates.
  • Investigated behavior under varying salt concentrations and loading rates.

    • Main Results:

    • Nucleosome unraveling occurs in at least two distinct stages.
    • The outer DNA wrap exhibits reversible, two-state hopping behavior under force.
    • The inner DNA wrap unraveling is a more complex process, not simply two-state.
    • The outer wrap is more sensitive to ionic strength changes than the inner wrap.

    Conclusions:

    • The mechanical properties of nucleosome DNA wraps differ significantly.
    • These findings provide insights into the energetics of nucleosome remodeling.
    • The differential sensitivity to ionic environment suggests distinct roles for inner and outer wraps in dynamic processes.