Long-range interactions of multiple DNA structural transitions within a common topological domain

Abstract

Local DNA conformations that are underwound with respect to the right-handed B form are favored in negatively supercoiled DNA. However, when multiple transitional events co-exist within a common topological domain, they must compete with one another for the available free energy of negative supercoiling. Recently we developed a general theoretical model capable of predicting the behavior at equilibrium of defined sequences in a variety of competitive situations. In the present work we have applied this theory to predict the formation of Z-DNA as a function of superhelicity in stretches of d(CG)m and d(CA)n when they are forced to compete with one another in the same plasmid. The observed behavior of these competing sequences is in close accord with theoretical predictions. These results indicate that sequences separated by large distances can effect the transitional behavior of each other in a complex manner which is independent of the relative orientation of the participating segments. The pattern of transitional events is strongly dependent on levels of DNA supercoiling, ambient conditions and on the nature and number of the sequences involved. Although in the present work we apply the model specifically to the Z-DNA conformational transition, the results of this study may have general relevance to a variety of biological processes in which the helical repeat of DNA is reversibly altered, including the initial steps in transcription, replication and recombination.