Entropic trap, surface-mediated combing, and assembly of DNA molecules within submicrometer interfacial confinement

Abstract

In this work, we report an alternative microfluidic approach to studying the motion of single DNA molecules in an electric field. Making use of a closely fitting droplet in a microchannel, DNA molecules can be confined within the submicrometer film beneath the droplet. Several dynamic events at the single-molecule level and self-assembly phenomena at mesoscales are observed. We find that DNA can be trapped and stretched at the entrance to the film due to entropic effects. After escaping the trap, DNA can exhibit cyclic stick-slip motion with a field-dependent mobility owing to interim anchoring to surface surfactants. We also observe that, by incorporation of surface modification effects with plasma oxidation, DNA can be combed onto the channel surface at sufficiently high fields. In this case, upon removing the field, as-stretched DNA molecules can aggregate into larger clusters or self-organize into mesoscale bundles aligned in the direction of the previously applied field. The physics underlying these phenomena is discussed in detail.