Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Poster Abstracts

14-POS Board 14 SEQUENCE-DEPENDENT CONFIGURATIONAL DYNAMICS OF BACTERIAL GENES Chanwoo Kim 1 ; Seungwon Lee 1 ; Jejoong You 2 ; Hajin Kim 1 ; 1 Ulsan National Institute of Science and Technology, School of Life Sciences, Ulsan, Chungcheongnam-do, South Korea 2 Institute of Basic Science, Center for Self-assembly and Complexity, Pohang, Gyeongsangbuk- do, South Korea Recent studies on the fundamental physical properties of DNA suggest that local nucleotide sequence, chemical modifications, and sequence motifs critically influence the physical properties, thus possibly controlling the geometric configuration of the DNA and its temporal changes. Such control of DNA geometry and dynamics may relate to the mechanism of assembling and organizing long DNAs and chromatin in the cells. Here, we employ single molecule fluorescence resonance energy transfer (smFRET), transmission electron microscopy (TEM), confocal fluorescence microscopy, and molecular dynamics simulations to study the conformation and dynamics of Escherchia coli genes. We show that the compaction and looping properties of the DNA sharply depend on the sequence composition and the density of GATC motifs which significantly increase the local rigidity. Further increase of the DNA rigidity was observed when the GATC motif is methylated at the N6 position of the adenine (GmeATC). We find that the modulation of the compaction and looping properties relate to the phase separation behaviors of DNA. Our results propose that the sequence structure and chemical modifications controlling the phase separation of DNA might play a mechanistic role in large scale genome organization.

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