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2 - Conformational transitions


The main form of the double helix, the B form, is stabilized by only weak hydrogen bonds and van der Waals interactions. If we also take into account the remarkable flexibility of the backbone of ssDNA, it is not surprising that depending on the solution conditions DNA can be found in various alternative forms. Conformational flexibility of DNA is needed for its functioning, since it facilitates speciflc DNA-DNA, DNA-RNA and DNA–protein interactions inside the cell. When we are changing solution conditions gradually, DNA can undergo transitions from one form to another. Studying these transitions has brought a lot of important information about DNA conformational flexibility and the stability of the various forms. This is why the conformational transitions have been a subject of biophysical investigation for decades. In this chapter we start from general theoretical analysis of the transitions, and then consider individual transitions: DNA melting or the helix–coil transition, B–A and B–Z transitions. We mainly consider only equilibrium properties of the transitions; the corresponding dynamic properties will be the subject of Chapter 4.

Theoretical analysis of conformational transitions in DNA

2.1.1 Preliminary remarks

A key concept of the theoretical description of conformational transitions that will be used in this chapter is a concept of a macrostate. It seems that Zimm and Bragg were the first to apply this approach to the analysis of the helix–coil transition in polypeptides (Zimm & Bragg 1959), although a few groups were moving in the same direction at that time. In this approach all microscopic states of a base pair (or nucleotides that can form the base pair) are divided into two groups, which correspond to the two DNA forms under consideration. The exact numbers of microstates in the macrostates and their corresponding energies are not specified in this approach. To apply it we only need to know the ratio of the statistical weights of the macrostates.

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