Probing Organization of Multiple Chains in Nanofluidic Cavities*

How do multiple interacting polymers behave in confined environments? This is a fundamental problem in confined polymer physics with important implications in a range of biological systems, from chromosomal segregation and plasmid distribution in dividing bacteria to chromatin organization. Here we use nanofluidics to trap multiple chains in cavity structures. Differential staining of the chains is used to independently assess the conformation of each chain, determine the degree of partitioning/mixing and assess coupled diffusion of the chain center-of-mass positions. Measurements are performed as a function of cavity dimension, salt concentration and polymer topology. In addition, we use varying chain size ratio to assess the degree to which small chains can interpenetrate large chains, a toy model of the phenomena of “nucleoid occlusion.”