Entropic localization of plasmids in nanofluidic compartments

Bacteria must stably partition their plasmids to their daughter cells upon division. While purely random partitioning can theoretically ensure stable transmission of plasmids to daughter cells, it is not clear that plasmid partitioning is random. Studies tracking plasmids in vivo show that multi-plasmid clusters present at the cell poles, but the roles played by the cell geometry and chromosome-plasmid interactions are still unclear. Here, we present a nanofluidic device with compartments simulating the confinement induced by a cell membrane. The compartments can be opened and closed by pneumatically actuating the thin membrane lid. The cavities are elliptical with a width varying from around 200 nm to 2 um. A differentially stained T4 DNA molecule and one plasmid molecule are introduced inside the compartment and monitored in real time from their fluorescence signals. We find that the plasmid prefers the peripheral of the cavity as has been observed in in vivo measurements in E. Coli, forming a ring shape distribution. In addition, as the cavity aspect ratio increases, the plasmid shows a preference for the cavity poles. Our results suggest that the free energy landscape formed by chain-chain interaction and the confinement geometry helps promote plasmid localization.