Chapter 3: DNA on surfaces

Linking number, twist and writhe are powerful concepts for understanding the geometry of supercoiled DNA. However, an important factor that can modulate DNA supercoiling is the wrapping of the DNA on a protein surface; the most well-known example is the nucleosome. In such cases, methods for measuring the twist of the DNA are influenced not only by the DNA conformation, but also by the shape of the curved surface on which the DNA lies. This chapter describes an alternative topological description of closed circular DNA, the surface-linking model, which was developed to address just these situations. The method relies on considering the difference between measurements made in two frames of reference: that of the DNA axis, and of the surface on which it lies. We describe the surface linking model in some detail, briefly describe its application in the case of DNA loops and sequence periodicities across whole genomes, and discuss the conformation of DNA in the nucleosome and the so-called linking number paradox.

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Figures

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