DNA topoisomerases are the magicians of the DNA world by allowing DNA strands or double helices to pass through each other, they can solve all of the topological problems of DNA in replication, transcription and other cellular transactions. Extensive biochemical and structural studies over the past three decades have provided molecular models of how the various subfamilies of DNA topoisomerase manipulate DNA. In this review, the cellular roles of these enzymes are examined from a molecular point of view.

The various problems of disentangling DNA strands or duplexes in a cell are all rooted in the double-helical structure of DNA. Three distinct subfamilies of enzymes, known as the DNA topoisomerases, have evolved to solve these problems. This review focuses on work in the past decade on the mechanisms and cellular functions of these enzymes. Newly discovered members and recent biochemical and structural results are reviewed, and mechanistic implications of these results are summarized. The primary cellular functions of these enzymes, including their roles in replication, transcription, chromosome condensation, and the maintenance of genome stability, are then discussed. The review ends with a summary of the regulation of the cellular levels of these enzymes and a discussion of their association with other cellular proteins.

Transcription of a right-handed double-helical DNA requires a relative rotation of the RNA polymerase and its nascent RNA around the DNA. We describe conditions under which the resistance to the rotational motion of the transcription ensemble around the DNA can be large. In such cases, the advancing polymerase generates positive supercoils in the DNA template ahead of it and negative supercoils behind it. Mutual annihilation of the positively and negatively supercoiled regions may be prevented by anchoring points on the DNA to a large structure, or, in the case of an unanchored plasmid, by the presence of two oppositely oriented transcription units. In prokaryotes, DNA topoisomerase I preferentially removes negative supercoils and DNA gyrase (topoisomerase II) removes positive ones. Our model thus provides an explanation for the experimentally observed high degree of negative or positive supercoiling of intracellular pBR322 DNA when DNA topoisomerase I or gyrase is respectively inhibited. We discuss the implications of our model in terms of supercoiling regulation, DNA conformational transitions, and gene regulation in both prokaryotes and eukaryotes.Plausible effects of transcription on the dynamics of the template DNA have been recognized for some time. Maal0e and Kjeldgaard (1) pointed out that as transcription proceeded along the helical template, it might be difficult for the RNA polymerase and its nascent RNA chain to turn around the DNA; thus the DNA might turn around its axis instead as the transcription apparatus tracks along.With the discovery of Escherichia coli DNA topoisomerase I, the possible requirement of a transcriptional "swivel" in the DNA was again raised (2). Such a swivel would allow a segment of the DNA being actively transcribed to rotate without turning the entire DNA molecule around its axis. Indirect evidence favoring such a possibility includes the finding that eukaryotic DNA topoisomerase I is often found to be associated with transcriptionally active genes (3-6).Whereas the possibility of turning the DNA during transcription is well-recognized, transcription is rarely viewed as a force that might actively supercoil DNA. Only special cases, in which the polymerase is interacting with a DNAbound regulatory protein, or when both the polymerase and the DNA are anchored on a cellular structure, have been considered in terms of DNA supercoiling driven by transcription (7,8). In this communication, we describe several cases in which transcription may lead to DNA supercoiling. We believe that the concepts presented here can explain a number of observations in the literature that have not been adequately interpreted. These and other implications of template supercoiling by transcription are discussed. THEORY AND MODELSBasic Considerations. Fig. 1 illustrates the basic mechanics of transcription. An RNA polymerase, together with its nascent RNA and RNA-bound proteins (ribosomes and newly synthesized proteins in prokaryotes and ribonucleoprotein complexes in eukaryotes), are tracking ...

The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an ATP-modulated clamp with two sets of jaws at opposite ends, connected by multiple joints. An enzyme with bound DNA can admit a second DNA duplex through one set of jaws, transport it through the cleaved first duplex, and expel it through the other set of jaws.