Single-chain compaction of long duplex DNA by cationic nanoparticles: modes of interaction and comparison with chromatin

J Phys Chem B. 2007 Mar 22;111(11):3019-31. doi: 10.1021/jp067926z. Epub 2007 Feb 28.

Abstract

The compaction of long duplex DNA by cationic nanoparticles (NP) used as a primary model of histone core particles has been investigated. We have systematically studied the effect of salt concentration, particle size, and particle charge by means of single-molecule observations-fluorescence microscopy (FM) and transmission electron microscopy (TEM)-and molecular dynamics (MD) simulations. We have found that the large-scale DNA compaction is progressive and proceeds through the formation of beads-on-a-string structures of various morphologies. The DNA adsorbed amount per particle depends weakly on NP concentration but increases significantly with an increase in particle size and is optimal at an intermediate salt concentration. Three different complexation mechanisms have been identified depending on the correlation between DNA and NPs in terms of geometry, chain rigidity, and electrostatic interactions: free DNA adsorption onto NP surface, DNA wrapping around NP, and NP collection on DNA chain.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cations / chemistry*
  • Chromatin / chemistry*
  • Chromatin / ultrastructure*
  • Computer Simulation
  • DNA / chemistry*
  • DNA / ultrastructure*
  • Microscopy, Electron, Transmission
  • Microscopy, Fluorescence
  • Nanoparticles / chemistry*
  • Nanoparticles / ultrastructure*
  • Nucleic Acid Conformation
  • Particle Size

Substances

  • Cations
  • Chromatin
  • DNA