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Sequence-Dependent Configurational Entropy Change of DNA upon Intercalation

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Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic, Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
* Corresponding author. Tel.: (+420) 220 410 311; e-mail: [email protected]
†Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems.
‡Karlsruhe Institute of Technology.
§Palacký University.
Cite this: J. Phys. Chem. B 2010, 114, 42, 13446–13454
Publication Date (Web):October 6, 2010
Copyright © 2010 American Chemical Society

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    Abstract Image

    We investigated the intercalation of an antitumor drug ellipticine into four adenine−thymine (AT) rich DNA duplexes with the focus on the configurational entropy, by means of molecular dynamics (MD) simulations. Two possible binding orientations of ellipticine in a DNA double helix were studied, and the orientation with the pyrrole nitrogen exposed into a major groove was identified as the more probable. The configurational entropy change of DNA is shown to contribute significantly to the binding free energy. The magnitude of this contribution depends on the exact DNA sequence. A detailed analysis revealed that the largest flexibility changes occurred in the sugar−phosphate backbone, resulting in an entropy gain in the most cases. The nucleobases were not involved in the changes of flexibility and entropy. BI/BII-like conformational transitions were observed after the intercalation of ellipticine, and the consequences of these transitions for the evaluation of entropy are discussed.

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    Structures of all studied DNA double helices and DNA...ellipticine complexes provided as PDB files. An extended version of Table 2 containing absolute values of entropy estimates for infinite simulation times is also available. This material is available free of charge via the Internet at

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