Organization and Dynamics of Multiple DNA Chains Confined in a Nanofluidic Compartment*

The dynamics of multiple chains interacting in a confined environment is a fundamental problem in polymer physics and a model system for understanding confinement in biological systems. Here we present a nanofluidic device with compartments that can be opened and closed via pneumatic actuation of a thin membrane lid. The compartments are elliptical in shape with widths and lengths varying from hundreds of nm to microns. Differentially stained chains are trapped inside the cavities and the chain interactions assessed by monitoring the chain conformation and positioning in real-time via fluorescence video-microscopy. We observe a transition between different dynamical states as the confinement is varied from quasi-0D (cavity confinement) to quasi 1-D (nanochannel confinement).