Mechanically heterogeneous DNA-catenanes

Recent years have witnessed an ever-increasing attention on the properties of topologically interlinked (catenated) ring polymers, including both naturally occurring biological catenated polymers, and synthetically produced DNA catenanes. Despite experimental progress, our fundamental knowledge of the theoretical physics of catenated ring polymers still lags substantially behind that of other polymeric or interlocked systems (e.g., rotaxanes). The focus here is on understanding the effects of intrinsic mechanical heterogeneity and environmental triggers like pH and ionic strength on the material properties of DNA catenane chains under equilibrium or flow. This work is computational in nature, proposing a two-level coarse-graining strategy for the DNA minicircles that constitute the building blocks of the DNA catenanes. The first level involves coarse-graining from an all-atom representation to a nucleotide level ("effective monomer"). Proceeding to a second level of coarse-graining, DNA minicircles are viewed as penetrable rings and all effective physical interactions are further reduced to a center-ofmass level, point-like description. Complementary to the computational approach, a collaboration with the experimental group of Dr. Emmanuel Stiakakis ((Forschungszentrum Jülich)) has been established, to provide a means of validation of these models. This work contributes to the fundamental understanding of the physics and the property-guided design of novel, mechanically heterogeneous DNA catenanes.