Stacking Interactions and DNA Intercalation英文电子书.pdf

11166 J. Phys. Chem. B 2009, 113, 11166–11172 Stacking Interactions and DNA Intercalation Shen Li,*,†,‡ Valentino R. Cooper,†,§ T. Thonhauser,†,| Bengt I. Lundqvist,⊥ and David C. Langreth† Department of Physics and Astronomy, Rutgers Uni Versity, Piscataway, New Jersey 08854-8019, Fred Hutchinson Cancer Research Center, Seattle, Washington 98019, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, Department of Physics, Wake Forest UniVersity, Winston-Salem, North Carolina 27109, and Department of Applied Physics, Chalmers Uni Versity of Technology, SE-412 96 Go¨teborg, Sweden Recei Ved: June 18, 2009 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 intercalat