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Title: Three-Dimensional Thermodynamic Simulation of Condensin as a DNA-Based Translocase
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.  more » « less
Award ID(s):
1816630 1664645
NSF-PAR ID:
10248732
Author(s) / Creator(s):
; ; ;
Editor(s):
Badrinarayanan, A.
Date Published:
Journal Name:
Methods in molecular biology
Volume:
2004
ISSN:
1064-3745
Page Range / eLocation ID:
291-318
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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