Competitive behavior of multiple, discrete B-Z transitions in supercoiled DNA.

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Abstract
Conformational transitions in topologically constrained duplex DNA necessarily affect and are affected by other transitional processes throughout the entire molecule. This conformational interdependence of discrete sequences within a given superhelical domain arises through a requisite competition for the free energy of supercoiling. Here we present a generalized statistical mechanical analysis of multiple, competing conformational equilibria in superhelical DNA. This model has been applied, using experimentally determined parameters, to the energetic coupling of two independent B-Z transitions. Specifically, we have monitored the extent of B-Z transition, as a function of negative superhelicity, in topoisomers of a plasmid containing two identical d(C-G)n inserts using two-dimensional gel electrophoresis. The theoretical results were found to be in good agreement with the experimental data, and we have used this model to predict the competitive behavior of B-Z transitions within sequences differing in length and sequence composition. This competition is shown to have a profound effect upon the B-Z equilibria of those sequences analyzed, resulting in a complex modulation in the extent of Z-DNA formation as a function of negative superhelicity. These theoretical and experimental results show that DNA sequences separated by large distances are capable of communicating structural information.