The well-known structure of DNA double helix provides an elegant mechanistic basis for storage and transmission of genetic information. However, the unwinding and rewinding of the duplex during the processes of DNA transactions can lead to topological entanglements that result in genome instability if left unresolved. Many other processes during DNA transactions including helical tracking and coiling of DNA to form higher order structures can also lead to topological complexities that are potentially deleterious to cells. DNA topoisomerases are nature's tools to resolve the problems of DNA entanglements by enabling topological transformations, thus regulating the structures of DNA/chromosomes and their associated cellular functions. The importance of these enzymes is also evidenced by the fact that they are ubiquitous in nature and their impairment due to genetic mutations results in deleterious effects including lethality in many organisms.

Topoisomerases tackle these seemingly complex problems by utilizing a simple yet elegant chemistry of reversible transesterification reactions. The active site tyrosine in these enzymes functions as a nucleophile to generate a transient break serving as DNA gate through which all topological transformations can occur. Our laboratory has generated fluorescence-labeled DNA substrate so that we can monitor the strand break and gate opening by topoisomerase using either single molecules measurements or under bulk conditions. These optical approaches to examine the steps in manipulating DNA structures by the enzyme have allowed us to design a facile high through-put screening platform for identifying potential anticancer drugs targeting DNA topoisomerases.