title: Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating.
abstract: DNA self-assembly has emerged as a new paradigm for design of biomimetic membrane channels. Several experimental groups have already demonstrated assembly and insertion of DNA channels into lipid bilayer membranes; however, the structure of the channels and their conductance mechanism have remained undetermined. Here, we report the results of molecular dynamics simulations that characterized the biophysical properties of the DNA membrane channels with atomic precision. We show that, while overall remaining stable, the local structure of the channels undergoes considerable fluctuations, departing from the idealized design. The transmembrane ionic current flows both through the central pore of the channel as well as along the DNA walls and through the gaps in the DNA structure. Surprisingly, we find that the conductance of DNA channels depend on the membrane tension, making them potentially suitable for force-sensing applications. Finally, we show that electro-osmosis governs the transport of druglike molecules through the DNA channels.
authors.affiliation: Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.
authors.forename: Jejoong
authors.initials: J
authors.lastname: Yoo
authors.affiliation: Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
mesh_terms: D004247:DNA / Q000737:chemistry*; D007473:Ion Channels / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D036103:Nanotechnology / Q000379:methods*
chemical_list: D007473:Ion Channels; D004247:DNA
keywords: DNA nanotechnology; electro-osmosis; ionic current; mechano-sensitive channels; molecular dynamics; nanopore