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Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

Benedetti, Fabrizio ; Japaridze, Aleksandre ; Dorier, Julien ; Racko, Dusan ; Kwapich, Robert ; Burnier, Yannis ; Dietler, Giovanni ; Stasiak, Andrzej

In: Nucleic Acids Research, 2015, vol. 43, no. 4, p. 2390-2399

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    Titre
    • Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling
    Auteur
    • Benedetti, Fabrizio. Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
    • Japaridze, Aleksandre. Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
    • Dorier, Julien. Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
    • Racko, Dusan. Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
    • Kwapich, Robert. Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
    • Burnier, Yannis. Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
    • Dietler, Giovanni. Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
    • Stasiak, Andrzej. Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Nucleic Acids Research, 2015, vol. 43, no. 4, p. 2390-2399. Oxford University Press
    Autre version électronique
    Classification
    • Santé
    Identifiant OAI-PMH
    • oai:doc.rero.ch:296169
    Summary
    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