Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex (Q1035328)

In difference topology experiments circular DNA is first incubated with the protein under study, in this paper Mu transposase (MuA), which binds the DNA. A second protein whose mechanism is well understood is added to the reaction. The effect of this is to change the topology of the DNA resulting in a knot or link. From this transformation and using the tangle calculus it is possible to deduce restrictions on the the topological structure of the protein of interest. This paper provides a formal topological framework for this analysis. The authors show that the results of a specific cited set of experiments allow one to deduce a unique biologically relevant solution for the topological structure of MuA. Specifically there is a unique rational tangle solution, which is also the unique solution with small crossing number.