title: Competitive behavior of multiple, discrete B-Z transitions in supercoiled DNA.
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.
authors.forename: R J
authors.initials: RJ
authors.lastname: Kelleher
authors.forename: M J
authors.initials: MJ
authors.lastname: Ellison
authors.forename: P S
authors.initials: PS
authors.lastname: Ho
authors.forename: A
authors.initials: A
authors.lastname: Rich
mesh_terms: D004247:DNA; D004278:DNA, Superhelical; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011089:Polydeoxyribonucleotides; D013816:Thermodynamics
chemical_list: D004278:DNA, Superhelical; D011089:Polydeoxyribonucleotides; C019530:poly(dC-dG); D004247:DNA