Chapter 6: Biological consequences of DNA topology

By the time you get to this chapter you will have a pretty good grasp of the concepts of DNA topology and will appreciate that it is an unavoidable issue when dealing with virtually any naturally-occurring DNA molecule. The purpose of Chapter 6 is to put DNA topology into the context of important biological processes: DNA replication, transcription and recombination. You will see how for some processes, e.g. initiation of bacterial DNA replication, supercoiling is an essential prerequisite for the reaction to occur, whereas for others, e.g. transcription elongation, it is a consequence of the reaction that has to be controlled. In general, supercoiling is a 'good thing' in cells, and is maintained and controlled, whereas knotting and catenation are 'bad things' to be systematically removed. This distinction is reflected in this chapter. Organisms go to a lot of trouble to control the topology of their DNA molecules as indicated by the number of DNA topoisomerases that have been identified (Chapter 5). In some cases there is redundancy with more than one enzyme being capable of carrying out the same reaction.

Most of the sections in Chapter 6 centre around supercoiling, as virtually all naturally-occurring DNA molecules seem to be supercoiled. With the exception of some thermophilic species, all organisms appear to maintain their DNA molecules in a negatively supercoiled state. From Chapter 2 you will see that this favours DNA unwinding and is likely to facilitate processes where proteins require access to the DNA bases, such as replication and transcription. The examples given in this chapter demonstrate that DNA topology is of fundamental importance for a wide range of biological processes. Indeed, virtually every reaction involving DNA is influenced by DNA topology, or has topological effects. There is a tendency to think of DNA merely as a code (G,A,T,C, etc) that functions like 'ticker-tape' to be translated into RNA and ultimately protein. While this has some merit from a genetic perspective, it is important also to be aware of the higher order structural features of DNA and how these have a profound effect on its function.

Click on the thumbnails below for full-size versions of the illustrations in Chapter 6.

Alternatively, you can download zip files containing all the figures for Chapter 6 (file 1 and file 2).

Figures

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