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SMC Complexes pp 291-318 | Cite as

Three-Dimensional Thermodynamic Simulation of Condensin as a DNA-Based Translocase

  • Josh Lawrimore
  • Yunyan He
  • Gregory M. Forest
  • Kerry BloomEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2004)

Abstract

Chromatin dynamics and organization can be altered by condensin complexes. In turn, the molecular behavior of a condensin complex changes based on the tension of the substrate to which condensin is bound. This interplay between chromatin organization and condensin behavior demonstrates the need for tools that allows condensin complexes to be observed on a variety of chromatin organizations. We provide a method for simulating condensin complexes on a dynamic polymer substrate using the polymer dynamics simulator ChromoShake and the condensin simulator RotoStep. These simulations can be converted into simulated fluorescent images that are able to be directly compared to experimental images of condensin and fluorescently labeled chromatin. Our pipeline enables users to explore how changes in condensin behavior alters chromatin dynamics and vice versa while providing simulated image datasets that can be directly compared to experimental observations.

Key words

Condensin Polymer dynamics simulator Chromatin Simulated fluorescent images Computational image analysis ChromoShake RotoStep Microscope Simulator 2 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Josh Lawrimore
    • 1
    • 2
  • Yunyan He
    • 3
  • Gregory M. Forest
    • 3
  • Kerry Bloom
    • 1
    Email author
  1. 1.Department of BiologyUniversity of North Carolina at Chapel HillChapel HillUSA
  2. 2.Curriculum in Genetics and Molecular BiologyUniversity of North Carolina at Chapel HillChapel HillUSA
  3. 3.Department of Mathematics and Biomedical EngineeringUniversity of North Carolina at Chapel HillChapel HillUSA

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