AFM investigation of Topological and Physical Properties of Kinetoplast DNA

Kinetoplast DNA (kDNA) is a two-dimensional network of topologically linked DNA molecules found in trypanosome parasites. Studying kDNA can improve our understanding of polymer

physics and their topology, particularly as an example of mechanically interlocked molecular rings (polycatenanes). The mechanisms of stiffness and flexibility within topologically

interlocked molecules are not fully understood. In this study, linked-ring structures are extracted from the kinetoplasts by dissolving the networks using restriction enzymes and scanned with an Atomic Force Microscope (AFM). The AFM images are analyzed to measure the persistence length of the DNA polycatenanes by mapping them onto the wormlike chain model. Here, we report on the properties of kinetoplast-derived polycatenanes, including apparent branched structures that form as well as their persistence length. Additionally, we discuss the results of a mathematical model that establishes that kinetoplast DNA can adopt a crossing-number-minimizing conformation.