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DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
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Anisotropy-Based Nucleosome Repositioning Assay.

Koan Briggs1, Gada Al-Ani2, Allen Eastlund1

  • 1Department of Physics and Astronomy, College of Liberal Arts and Sciences, The University of Kansas, Lawrence, KS, USA.

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|July 5, 2018
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Summary
This summary is machine-generated.

Chromatin remodelers use ATP to slide nucleosomes, regulating gene expression and DNA repair. Analyzing kinetic data with nonlinear least squares (NLLS) reveals the rate and ATP coupling of nucleosome repositioning.

Keywords:
ATPaseChromatin remodelerFluorescence anisotropyMotor proteinNucleosome repositioningSequential n-step mechanism

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Area of Science:

  • Molecular biology
  • Biochemistry
  • Genomics

Background:

  • Eukaryotic DNA is packaged into nucleosomes, limiting access for transcription and repair.
  • Chromatin remodelers are ATP-dependent molecular motors that alter nucleosome structure.
  • These remodelers are crucial for gene expression regulation and maintaining genomic integrity.

Purpose of the Study:

  • To analyze kinetic data from nucleosome sliding experiments.
  • To estimate the rate of nucleosome repositioning.
  • To determine the stoichiometry of ATP binding and hydrolysis coupled to nucleosome sliding.

Main Methods:

  • Monitoring changes in fluorescence anisotropy of DNA-bound fluorophores during nucleosome sliding.
  • Indirectly monitoring ATP hydrolysis by chromatin remodelers.
  • Simultaneous global nonlinear least squares (NLLS) analysis of kinetic data.

Main Results:

  • Quantification of the macroscopic rate of nucleosome repositioning.
  • Estimation of the stoichiometry of ATP hydrolysis coupled to nucleosome sliding.
  • Validation of "n-step" sequential mechanisms for nucleosome remodeling.

Conclusions:

  • NLLS analysis provides accurate estimates of nucleosome repositioning rates.
  • The study elucidates the coupling mechanism between ATP turnover and nucleosome sliding.
  • This kinetic analysis framework is essential for understanding chromatin dynamics.