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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
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Why Do Nucleosomes Unwrap Asymmetrically?

Lennart de Bruin1, Marco Tompitak1, Behrouz Eslami-Mossallam1,2

  • 1Institute Lorentz for Theoretical Physics, Leiden University , Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.

The Journal of Physical Chemistry. B
|March 19, 2016
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Summary
This summary is machine-generated.

Nucleosomes (DNA-protein complexes) show asymmetric responses to force due to DNA mechanics. This suggests DNA sequence can tune nucleosome properties for genomic functions.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genomics

Background:

  • Nucleosomes are fundamental to eukaryotic DNA organization and function.
  • Understanding nucleosome stability and dynamics is crucial for processes like gene regulation and replication.
  • Previous micromanipulation experiments have provided insights into nucleosome behavior under tension.

Purpose of the Study:

  • To provide a theoretical explanation for the asymmetric unwrapping of nucleosomes from the 601 DNA sequence under external forces.
  • To investigate the role of DNA mechanics in nucleosome force response.
  • To propose a new perspective on nucleosomes as tunable DNA-protein complexes.

Main Methods:

  • Utilized a computational nucleosome model.
  • Analyzed the mechanical properties of short DNA stretches within the nucleosome.
  • Interpreted experimental findings on nucleosome unwrapping dynamics.

Main Results:

  • Demonstrated that nucleosomes wrapped with the 601 sequence exhibit highly asymmetric force responses, always unwrapping from the same end.
  • Identified differences in DNA mechanics between two short segments of the wrapped DNA as the cause of this asymmetry.
  • Showed that the base-pair sequence influences nucleosome mechanical properties.

Conclusions:

  • The sequence-dependent mechanical properties of DNA within nucleosomes explain their asymmetric response to force.
  • Nucleosome physical properties, such as force response, can be locally tuned by the DNA sequence.
  • This suggests nucleosomes are a diverse set of complexes whose properties are adapted for specific genomic roles.