5 DNA Supercoiling and Unusual Structures

Abstract

I. INTRODUCTION What are the structural consequences of DNA supercoiling? Until recently, the importance of the problem was generally underestimated because the available data gave relatively low absolute values for the degree of DNA supercoiling inside the cell. Many people, I concluded, considered the dramatic changes in DNA structure at high levels of supercoiling as physicochemical tricks that were not directly relevant to biology. The only excuse for continuing the studies stemmed from the hope that the phenomena observed under those artificial conditions pointed to the ability of DNA to form unusual structures, other than the canonical Watson-Crick double helix, under the action of special proteins. The attitude has changed after the recent demonstration that a high local degree of supercoiling can occur as a consequence of the double-helical nature of DNA (Giaever and Wang 1988; Wu et al. 1988). We now understand that the overall degree of DNA supercoiling in the cell is much less relevant from a biological viewpoint and that the local transient degree of supercoiling may be much higher than the most ambitious physicochemist could ever dream of. Thus, we have to study the structural consequences of DNA supercoiling to understand the biological significance of DNA topology and to elucidate the structural potential of DNA. Supercoiling may be introduced into linear DNA provided both ends are fixed so that the DNA strands cannot rotate with respect to one another. Throughout this chapter, however, we restrict ourselves to the case of closed circular DNA, which is commonly...