Topological Analysis of Mu-Transposition

Abstract

An n-string tangle is a three dimensional ball with n-strings which are properly embedded in the ball. In early 90's, C. Ernst and D. Sumners first used a tangle to describe a DNA-protein complex. In this model, DNA is represented by a string and protein is represented by a ball. Mu is a protein which binds to DNA at three sites and a DNA-Mu complex is called Mu-transpososome. Knowing the DNA topology within Mu-transpososome is very important to understand DNA transposition by Mu protein. In 2002, Pathania et al. determined that the DNA configuration within the Mu transpososome is three branched and five noded [12]. In 2007, Darcy et al. analyzed this by using mathematical tangle and concluded that the three branched and five noded DNA configuration is the only biologically reasonable solution [4]. In this paper, based on the result of Pathania et al. and Darcy et al., the author determines the DNA topology within the DNA-Mu complex after the whole Mu transposition process. Furthermore, a new experiment is designed which can support the Pathania et al.'s result. The result of this new experiment is predicted through mathematical knot thory.