title: Stacking interactions and DNA intercalation.
abstract: The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair-base-pair interactions and that of the stacked intercalator-base-pair system. The most notable result is the paucity of torque, which so distinctively defines the twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observed proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair-intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.
authors.affiliation: Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854-8019, USA. sl2@fhcrc.org
authors.forename: Shen
authors.initials: S
authors.lastname: Li
authors.forename: Valentino R
authors.initials: VR
authors.lastname: Cooper
authors.forename: T
authors.initials: T
authors.lastname: Thonhauser
authors.forename: Bengt I
authors.initials: BI
authors.lastname: Lundqvist
authors.forename: David C
authors.initials: DC
authors.lastname: Langreth
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D008958:Models, Molecular
chemical_list: D007364:Intercalating Agents; D004247:DNA