Stacking Interactions and DNA Intercalation

Shen Li, Valentino R. Cooper, T. Thonhauser, Bengt Lundqvist, David Langreth

Research output: Contribution to journalJournal articleResearchpeer-review

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 call provide valuable information for future nonempirical studies of DNA intercalation dynamics.
Original languageEnglish
JournalJournal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical
Volume113
Issue number32
Pages (from-to)11166-11172
ISSN1520-6106
DOIs
Publication statusPublished - 2009
Externally publishedYes

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