Journal article
Stacking Interactions and DNA Intercalation
Department of Physics and Astronomy, Rutgers University, 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 University of Technology, SE-412 96 Göteborg, Sweden
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.
| Language: | English |
|---|---|
| Publisher: | American Chemical Society |
| Year: | 2009 |
| Pages: | 11166-11172 |
| ISSN: | 15205207 and 15206106 |
| Types: | Journal article |
| DOI: | 10.1021/jp905765c |
