Effect of nanochannel geometry on DNA structure in the presence of macromolecular crowding agent

Nano Lett. 2011 Nov 9;11(11):5047-53. doi: 10.1021/nl203114f. Epub 2011 Oct 14.


We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics simulations reproduce trends seen in the experiments and allow us to develop a deeper understanding of the key physics at play in these systems. It is proposed that the occupancy of free volume next to the channel wall by crowders causes an effective reduction in confining dimensions of the channel that initially swells DNA in nanoconfinement.

Publication types

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

MeSH terms

  • Computer Simulation
  • DNA / chemistry*
  • DNA / ultrastructure*
  • Macromolecular Substances / chemistry*
  • Materials Testing
  • Models, Chemical*
  • Models, Molecular
  • Molecular Conformation
  • Nanostructures / chemistry*
  • Nanostructures / ultrastructure*
  • Particle Size


  • Macromolecular Substances
  • DNA