Submission of this paper to the Faculty predates date of submission to the Digital Commons. This document was received by the Digital Commons on August 29, 2007 and posted on March 4, 2008. Original document was submitted as an honors thesis requirement.

Document Type



Topoisomerases are enzymes that change the topological state of DNA by catalyzing the cleavage, subsequent strand passage and religation of either one or both strands of DNA during DNA replication and transcription. This research thesis focused on Escherichia coli DNA topoisomerase IA, an enzyme largely responsible for the maintenance of supercoiling and the specific relaxation of negative supercoils in E. coli DNA. The various types of topoisomerases and their functions were discussed. As a basis for this paper, some of the structural properties not yet determined in topoisomerase IA were mentioned with respect to the catalytic mechanism. A description was given of the methods used for laboratory research, Monte Carlo simulations. The goals of this research, both short-term and long-term, were also discussed. Known background information about topoisomerase IA was given in detail with regard to the enzyme’s structure and catalytic mechanism, followed by a discussion on the interaction of ions with the enzyme throughout its catalytic mechanism. The results of Monte Carlo simulation data were presented in the thesis, and a discussion on these results was given along with the future hopes of this important research.