Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization

Nano Lett. 2017 Mar 8;17(3):1938-1948. doi: 10.1021/acs.nanolett.6b05294. Epub 2017 Feb 16.

Abstract

Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understand the link between genetic regulation, DNA structure, and topology. Here, we study very large supercoiled dsDNA using high-resolution characterization, theoretical modeling, and molecular dynamics calculations. We unveil a new type of highly ordered DNA organization forming in the presence of attractive DNA-DNA interactions, which we call hyperplectonemes. We demonstrate that their formation depends on DNA size, supercoiling, and bacterial physiology. We compare structural, nanomechanic, and dynamic properties of hyperplectonemes bound by three highly abundant nucleoid-associated proteins (FIS, H-NS, and HU). In all these cases, the negative supercoiling of DNA determines molecular dynamics, modulating their 3D shape. Overall, our findings provide a mechanistic insight into the critical role of DNA topology in genetic regulation.

Keywords: DNA; FIS; H-NS; HU; nucleoid associated proteins; plectonemes; self-organization; supercoiling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Bacterial / chemistry
  • DNA, Bacterial / ultrastructure*
  • DNA, Superhelical / chemistry
  • DNA, Superhelical / ultrastructure*
  • Escherichia coli / chemistry
  • Escherichia coli / ultrastructure*
  • Microscopy, Atomic Force
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation

Substances

  • DNA, Bacterial
  • DNA, Superhelical