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

N.N. Vtyurina, D. Dulin, M.W. Docter, A.S. Meyer, N.H. Dekker, E.A. Abbondanzieri

Research output: Contribution to JournalArticleAcademicpeer-review

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
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number18
DOIs
Publication statusPublished - 3 May 2016
Externally publishedYes

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