Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation.

ABSTRACT: Topological constraints, such as those associated with DNA supercoiling, play an integral role in genomic regulation and organization in living systems. However, physical understanding of the principles that underlie DNA organization at biologically relevant length scales remains a formidable challenge. We develop a coarse-grained simulation approach for predicting equilibrium conformations of supercoiled DNA. Our methodology enables the study of supercoiled DNA molecules at greater length scales and supercoiling densities than previously explored by simulation. With this approach, we study the conformational transitions that arise due to supercoiling across the full range of supercoiling densities that are commonly explored by living systems. Simulations of ring DNA molecules with lengths

SUBMITTER: Krajina BA 

PROVIDER: S-EPMC5052444 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature