title: Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.
abstract: DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA-DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.
authors: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland.
authors: Fabrizio
authors: F
authors: Benedetti
authors: Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland.
authors: Aleksandre
authors: A
authors: Japaridze
authors: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland.
authors: Julien
authors: J
authors: Dorier
authors: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland Polymer Institute of the Slovak Academy of Sciences, 845 41 Bratislava, Slovakia.
authors: Dusan
authors: D
authors: Racko
authors: Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland Department of Medical Physics, University of Silesia in Katowice, 40-007 Katowice, Poland.
authors: Robert
authors: R
authors: Kwapich
authors: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland.
authors: Yannis
authors: Y
authors: Burnier
authors: Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland.
authors: Giovanni
authors: G
authors: Dietler
authors: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland Andrzej.Stasiak@unil.ch.
authors: Andrzej
authors: A
authors: Stasiak
mesh_terms: D004247:DNA / Q000737:chemistry / Q000648:ultrastructure; D004270:DNA, Circular / Q000737:chemistry; D004278:DNA, Superhelical / Q000737:chemistry*; D004742:Enhancer Elements, Genetic; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic
chemical_list: D004270:DNA, Circular; D004278:DNA, Superhelical; D004247:DNA
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