Hysteresis in DNA compaction by Dps is described by an ising model

Natalia N. Vtyurina, David Dulin, Margreet W. Docter, Anne S. Meyer, Nynke H. Dekker, Elio A. Abbondanzieri

Research output: Contribution to journalArticleScientificpeer-review

12 Citations (Scopus)
38 Downloads (Pure)

Abstract

In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps-DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps. Real-time in vitro studies demonstrated a highly cooperative process of Dps binding characterized by an abrupt collapse of the DNA extension, even under applied tension. Surprisingly, we also discovered a reproducible hysteresis in the process of compaction and decompaction of the Dps-DNA complex. This hysteresis is extremely stable over hour-long timescales despite the rapid binding and dissociation rates of Dps. A modified Ising model is successfully applied to fit these kinetic features. We find that long-lived hysteresis arises naturally as a consequence of protein cooperativity in large complexes and provides a useful mechanism for cells to adopt unique epigenetic states.

Original languageEnglish
Pages (from-to)4982-4987
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number18
DOIs
Publication statusPublished - 3 May 2016

Keywords

  • Cooperativity
  • DNA condensation
  • Dps
  • Hysteresis
  • Ising model

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