Controlling the conformations and transport of DNA by free energy landscaping

We demonstrate free energy landscaping, a method for controlling the transport and conformations of DNA in nanofluidic devices with a nanotopography. A device that funnels molecules into traps where they adopt the shapes of letters illustrates the principle. We analyze how the nanotopography establishes regions of lower free energy and how entropic forces compete with advection, Brownian motion, and, importantly, excluded volume interactions; a rise in the density of DNA can be induced to facilitate its escape from a trap at a controlled location. An ability to guide DNA into solvent-permeable traps makes free energy landscaping applicable to genetic analyses. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3673277]