Brownian motion of DNA confined within a two-dimensional array.

Linear DNA molecules are visualized while undergoing Brownian motion inside media patterned with molecular-sized spatial constraints. The media, prepared by colloidal templating, trap the macromolecules within a two-dimensional array of spherical cavities interconnected by circular holes. Across a broad DNA size range, diffusion does not proceed by the familiar mechanisms of reptation or sieving. Rather, because of their inherent flexibility, DNA molecules strongly localize in cavities and only sporadically "jump" through holes. Jumping closely follows Poisson statistics. By reducing DNA's configurational freedom, the holes act as molecular weight-dependent entropic barriers. Sterically constrained macromolecular diffusion underlies many separation methods and assumes an important role in intracellular and extracellular transport.