Single molecule visualizations of polymer partitioning within model pore geometries

Probing the thermodynamics of polymer confinement in small pores, single DNA molecules were imaged by fluorescence microscopy as they partitioned within a pair of adjacent interconnected spherical cavities prepared by the colloidal templating method. This method produces pores of precisely known geometry and controlled level of confinement. As expected, a polymer weakly or moderately confined by cavities of unequal diameter was observed to maximize its configurational entropy by partitioning toward the larger cavity. The polymer's cavity-to-cavity partition coefficient could be derived from the visualized bias in cavity occupation, and segmental excluded volume notably influences how this coefficient depends on chain length and two cavity sizes. A DNA molecule strongly confined within a pair of equal-sized cavities predominately adopts "bridging" configurations, splitting its segments between the two cavities. Segmentai excluded-volume stabilizes such configurations; the stability reveals that a chain must overcome a doubly peaked energy barrier to move between cavities.