A topological analysis of difference topology experiments of condensin with Topoisomerases II

An experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the Mu transpososome. However, difference topology experiments can be difficult and time-consuming. We discuss a modification that greatly simplifies this experimental technique. This simple experiment involves using a topoisomerase to trap DNA crossings bound by a protein complex and then running a gel to determine the crossing number of the knotted product(s). We develop the mathematics needed to analyze the results and apply these results to model the topology of DNA bound by 13S condensin and by the condensin MukB.\n\nSUMMARY STATEMENTTangles are used to model protein-DNA complexes: A 3-dimensional ball represents protein while strings embedded in this ball represent protein-bound DNA. We use this simple model to analyze experimental results.