📝 SummarXiv

Abstract

Assemblies of ring DNA and proteins, such as kinetoplast DNA (kDNA) and the chainmail-like network of the HK97 bacteriophage capsid, form "Olympic" topologies that govern the dynamics of gene-regulatory proteins, cellular metabolites, and viral genomes. Yet the pore sizes that control transport and diffusion in these topologically linked networks remain poorly quantified. Here, using coarse-grained simulations of idealized square (SQR) and hexagonal (HEX) lattice catenated two-dimensional Olympic networks, we measure pore size as the radius of the largest rigid tracer that can pass through an aperture and delineate how backbone bending stiffness and topological tension regulate this structure. We identify two competing regulators: (i) ring entropic elasticity, which enlarges pores at low stiffness, and (ii) ring rotation angle, which reduces pore size at high stiffness. Their competition yields bimodal pore size distributions over a defined parameter range. Network geometry further modulates spatial correlations in pore size and the pore size autocorrelation time, predicting distinct propagation of perturbations in isostatic (SQR) versus hypostatic (HEX) architectures. These results provide testable predictions for enzyme diffusion kinetics and cargo release in natural or synthetic catenane DNA networks and mechanically interlocked capsid proteins, and offer a theoretical framework for interpreting FRAP (fluorescence recovery after photobleaching) and SMT (single-molecule tracking) measurements in topologically catenated biopolymer networks.