Abstract

DNA is known to be a highly polymorphic molecule, capable of assuming several alternate conformations in addition to the standard Watson-Crick B-form. These include states of strand separation, left handed helices, cruciforms, and three- and four-stranded structures. Although the B-form is its default conformation in vivo, regions within genomic DNA can be driven into alternate structures by the superhelicity imposed on the molecule by enzymatic activities and by transcription. This talk will present theoretical analyzes of several types of transitions, and of competitions among them. The predicted genomic distributions of locations susceptible to different types of superhelical transitions will be shown, and their statistical significances will be assessed. Several situations will be described where transitions to alternate structures serve biological roles in either normal or pathological processes.