Formation of DNA toroids inside confined droplets adsorbed on mica surfaces

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 May;79(5 Pt 1):051912. doi: 10.1103/PhysRevE.79.051912. Epub 2009 May 18.

Abstract

We report observations of in vitro DNA compaction into toroids in the absence of any condensing agent. The DNA toroid formation is induced by geometry confinement from microdroplets on mica surfaces. With AFM imaging we show that the confined DNA molecules may take the form of random coils or semiordered folded loops with large microdroplets, while they readily take the form of compact and ordered toroids when the microdroplet sizes are small enough. To better understand these phenomena, we carried out coarse-grained Brownian dynamics simulation, obtaining results that were in good agreement with the experimental observations. The simulation reveals that the toroid formation is sensitive to not only the microdroplet size, but also the DNA stiffness.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aluminum Silicates / chemistry*
  • Computer Simulation
  • DNA / chemistry*
  • DNA / ultrastructure*
  • Models, Chemical*
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Solutions
  • Surface Properties

Substances

  • Aluminum Silicates
  • Solutions
  • DNA
  • mica