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- W2004207780 abstract "Cells must package their chromosomes within a volume whose characteristic length is orders of magnitude smaller than the genomic length. When sufficiently twisted, DNA assumes a supercoiled form, aiding in this necessary compaction, as suggested in the case of Caulobacter crescentus. Given the crucial role supercoiling plays in bacterial DNA packaging, an elucidation of supercoiling structure and dynamics under confinement promises to shed light on critical living processes during replication as well as genome accessibility during transcription. We explore the structure and dynamics of supercoiled DNA by modeling the strand as a self-interacting, elastic beaded chain with twist and conduct Brownian Dynamics simulations under various geometries and degrees of confinement. The mean end-to-end distance between DNA segments exhibits a scaling of 0.25 with genome contour length, consistent with recent experiments in Caulobacter and suggesting a randomly branched supercoiled configuration. The scaling subsequently becomes linear at lengths comparable to the size of the enclosure. The mean-distance dynamic behavior at various length scales is highly sensitive to degree of confinement, and we identify the biologically relevant time scales of relaxation. Short genome lengths relax relatively fast with power-law scaling at all confinements while highly confined DNA is impeded from fully exploring its configurational space, resulting in delayed relaxation at large length scales. In this regime, the DNA segments become effectively quenched, resembling a stiff, glassy state that prohibits large-scale movement. We delineate the length-dependent transitions between these dynamic states and discuss their biological consequences in light of genome accessibility and reorganization." @default.
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- W2004207780 date "2012-01-01" @default.
- W2004207780 modified "2023-09-30" @default.
- W2004207780 title "Structure and Dynamics of Supercoiled DNA in Confinement" @default.
- W2004207780 doi "https://doi.org/10.1016/j.bpj.2011.11.1541" @default.
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