Confinement driven spatial organization of semiflexible ring polymers: Implications for biopolymer packaging

Abstract

We investigate the conformational properties of a semiflexible ring polymer in confined spaces. Taking into account the competing interplay between configurational entropy, bending energy and excluded volume, we elucidate the role that different geometrical constraints can play in shaping the spatial organization of biopolymers. While elongated, rod-like geometries reduce the amount of chain overcrossings and induce a pronounced ordering with respect to the long axis of the surrounding envelope, there exists no preferred orientational axis in the case of spherical confinement. Upon increasing the system density and the rigidity of the chain, the polymer migrates from the center of the accessible space towards the surrounding surface, forming a spool-like structure known for DNA condensation within viral capsids. The existence of distinguished loop sizes for different confining geometries might influence co-localization in biopolymers necessary for the genome-wide coordination of gene expression. Thus, the advantages of certain geometric constraints, such as spherical confinement of viral DNA in a capsid or the rod-shaped envelope of the circular chromosome in Escherichia coli could be one driving force for controlling proper biological functioning.