Entropic localization of multiple plasmids in a nanofluidic compartment

Bacteria typically have multiple copies of plasmids distributed in the compact intracellular environment. In vivo studies show that plasmids are not distributed randomly, instead they form clusters at the nucleoid circumference. Here, using a nanofluidic system that enables confinement variation based on pneumatic actuation of a thin membrane lid, we confine multiple plasmids along with a larger DNA molecule inside nano-compartments of varying anisotropy. The plasmids and larger DNA are differentially stained so they can be differentiated within the confined volume. We find that polymer-polymer excluded volume interactions combined with interaction with the compartment boundary lead to a spontaneous organization mimicking the biological system, with plasmids preferring the compartment periphery and poles. Increasing the compartment anisotropy leads to a stronger polar preference. In addition, we explore the effect of adding small molecules (dextran) to simulate the effect of molecular crowding.