SINGLE-MOLECULE STUDIES ON EUKARYOTIC TOPOISOMERASE II AND MECHANICAL PROPERTIES OF EUKARYOTIC CHROMATIN

Abstract

DNA replication inevitably encounters topological impasses created from the double helical structure of double stranded DNA. Incomplete resolution of the supercoils generated during fork progression leads to intertwining, or catenation, of the two sister chromatids which in turn leads to deleterious downstream effects such as aneuploidy. While biochemical aspects of regulation of catenation prevention and topoisomerase II, the enzyme primarily responsible for resolving supercoils during replication, activity on naked DNA have been deeply explored, the role of mechanical properties of chromatin and topoisomerase II activity on eukaryotic chromatin in its highly compacted form has been largely overlooked. Here I present single-molecule studies that provide insight into the effect of chromatin compaction via formation of nucleosomes in eukaryotic DNA replication and topoisomerase activity. First is the characterization of torsional mechanics of eukaryotic chromatin and its consequences followed up by observation of topoisomerase II activity on nucleosomal DNA. Secondly, I suggest a methodology to dissect the kinetic details of topoisomerase II activity and use it to observe response of the enzyme in physiologically relevant magnesium concentrations.