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Strand separation of the DNA double helix and its re-formation in a precisely ordered fashion is fundamental to life processes, ranging from metabolism in bacteria to social and sexual behavior in humans. Assessing the propensity of DNA to strand-separate under biologically relevant conditions, therefore, is an important problem. Common methods of assessing strand separation using local DNA sequence information (A+T content/thermodynamic stability) are not relevant, for two reasons: First, strand separation in vivo happens under isothermal conditions, so there are no changes of temperature to drive a thermal denaturation ("melting"). Second, DNA is held under regulated negative superhelicity in vivo, which couples the strand opening behaviors of all the base pairs that experience them. This coupling can occur over long distances, extending over many kilobases. Therefore, to accurately assess strand separation, the interplay between local properties (pair bonding, stacking energies and so on) and the long range coupling induced by superhelical stress energies needs to be considered. Hence, not only the local sequence, but also the genomic context in which a given sequence of interest is located needs to be taken into account. We use a calculation method that has empirically determined parameters (there are no free variables) to accurately evaluate energetic requirements of any given region of the DNA duplex to strand separate. A brief description of the method will be followed by examination of strand separation and its role in a wide variety of organisms and phenomena ranging from origins of replication in yeast to sexual and social behavior in humans.

more info under http://cse.ucdavis.edu/csseminar