Nanopore Translocation of Topologically Linked DNA Catenanes

Abstract

The electrical signal associated with a biopolymer translocating through a nanoscale pore depends depends on the size, topology, and configuration of each molecule. Building upon recent interest in using solid-state nanopores for studying the topology of knotted and supercoiled DNA, we present the first experimental observations of topologically linked catenanes translocating through a solid-state nanopore. Using restriction enzymes, linked circular molecules were isolated from the mitochondrial DNA of Crithidia fasciculata, a structure known as a kinetoplast that is comprised of thousands of topologically interlocked minicircles. Digested kinetoplasts produce a spectrum of catenane topologies, which are identified from their nanopore translocation signals by spikes in the blockade current associated with the topological linkages. We identify the translocation signatures of 2-catenanes, linear and triangular 3-catenanes, and several types of 4- and 5-catenanes as well as more complex structures. Measurements of the translocation time of 2- and 3-catenanes suggest that topological friction between the linkages and the pore slows the translocation time of these structures, as predicted in recent simulations.