DNA-DNA interactions in tight supercoils are described by a small effective charge density

Phys Rev Lett. 2010 Oct 8;105(15):158101. doi: 10.1103/PhysRevLett.105.158101. Epub 2010 Oct 4.

Abstract

DNA-DNA interactions are important for genome compaction and transcription regulation. In studies of such complex processes, DNA is often modeled as a homogeneously charged cylinder and its electrostatic interactions are calculated within the framework of the Poisson-Boltzmann equation. Commonly, a charge adaptation factor is used to address limitations of this theoretical approach. Despite considerable theoretical and experimental efforts, a rigorous quantitative assessment of this parameter is lacking. Here, we comprehensively characterized DNA-DNA interactions in the presence of monovalent ions by analyzing the supercoiling behavior of single DNA molecules held under constant tension. Both a theoretical model and coarse-grained simulations of this process revealed a surprisingly small effective DNA charge of 40% of the nominal charge density, which was additionally supported by all-atom molecular dynamics simulations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biomechanical Phenomena / drug effects
  • DNA, Superhelical / chemistry*
  • DNA, Superhelical / metabolism*
  • Molecular Dynamics Simulation
  • Monte Carlo Method
  • Salts / pharmacology
  • Static Electricity*

Substances

  • DNA, Superhelical
  • Salts