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Histone-DNA binding free energy cannot be measured in dilution-driven dissociation experiments
A Thåström1, J M Gottesfeld, K Luger
1Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208-3500, USA.
Biochemistry
|January 21, 2004
Summary
Dilution experiments measure nucleosome kinetic stability, not absolute equilibrium affinity. Nucleosome assembly/disassembly is not always reversible, complicating stability measurements.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Nucleosomes are fundamental units of DNA packaging in eukaryotes.
- Previous studies focused on relative histone-octamer DNA binding affinities, not absolute free energy.
- Recent methods aimed to measure absolute nucleosome stability via dilution experiments.
Purpose of the Study:
- To determine if dilution experiments can accurately measure absolute histone-DNA binding affinity.
- To investigate the reversibility of nucleosome assembly/disassembly under specific conditions.
- To assess the validity of using simple equilibrium models for nucleosome stability.
Main Methods:
- Quantitative analysis of nucleosome dissociation in dilution experiments.
- Testing nucleosome assembly/disassembly under varying salt concentrations and temperatures.
- Modeling nucleosome dissociation using a noncooperative equilibrium model.
Main Results:
- Nucleosome assembly/disassembly was found to be not strictly reversible under tested conditions.
- Increased salt or temperature induced cooperative behavior, invalidating simple equilibrium models.
- Dilution experiments accurately reflect kinetic stability, not thermodynamic equilibrium affinity.
Conclusions:
- Dilution experiments provide valuable insights into kinetic stability of nucleosomes.
- These experiments do not yield absolute equilibrium affinities due to non-reversible processes.
- Kinetic stability is functionally relevant in vivo and may or may not correlate with thermodynamic stability.
