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Chapter 2: DNA supercoiling
Chapter 1 describes the classical double-helical structure of DNA, and the local alterations of that structure that can occur as a consequence of specific nucleotide sequences. In Chapter 2, we move on to the main subject of the book, the supercoiling of DNA, a global alteration of structure that arises directly from the double-helical nature of the molecule.
We begin with a historical discussion of the problem of replication of a double-helical template and the discovery of supercoiling in the circular DNA of polyoma virus. The technicalities of supercoiling, including the concepts underlying linking number, twist and writhe are then discussed in some detail. We consider how supercoiling in circular DNA has been analysed by 1-D and 2-D gel electrophoresis and describe the effects of solution conditions, temperature and DNA-binding molecules on the conformation of supercoiled DNA. Different approaches to the thermodynamics of supercoiling are then described, including ethidium bromide binding, analysis of the equilibrium Gaussian distribution of topoisomers, and the effects of solution conditions and DNA length on the free energy of supercoiling. This then leads directly into consideration of the physical deformations underlying supercoiling (bending and twisting of the DNA helix) and the theoretical methods, including Monte Carlo simulations, that have been used to analyse the conformation of circular DNA. We finally describe how the free energy associated with supercoiling can stabilise alternative structures in DNA, using the formation of a region of Z-DNA as an example.
Click on the thumbnails below for full-size versions of the illustrations in Chapter 2.
Alternatively, you can download zip files containing all the figures for Chapter 2 (file 1, file 2, file 3, and file 4).
Figures
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