- Macromolecules confined within nanoporous surroundings experience entropic trapping (ET) when their dimensions approach the average pore size, leading to emergence of transport behavior that can be immensely beneficial (e.g., a counterintuitive trend of increasing separation efficiency with DNA size during gel electrophoresis) . But the noisy uncorrelated process by which the embedded macromolecules discretely hop from pore to pore contributes additional dispersion that detrimentally impacts most practical applications. Here show how the same dynamics governing phenomena as diverse as global climate change and sensory perception can be exploited to direct macromolecular transport through nanoporous surroundings. We demonstrate this in the context of gel electrophoresis by establishing a resonance condition that synchronizes the otherwise noisy uncorrelated motion of DNA between pores in the matrix. Surprising consequences include simultaneous transport of different-sized molecules in opposite directions, and a counterintuitive inverted size dependence of separation efficiency. We further show how DNA binding interactions can be sensitively probed by exploiting conformation dependence of resonance. These phenomena can be easily accessed in ordinary hydrogels (as opposed to idealized planar nanomachined topologies), offering a direct pathway to implement them in a host of useful settings.