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Research Letters in Physical Chemistry
Volume 2007 (2007), Article ID 60623, 5 pages
http://dx.doi.org/10.1155/2007/60623
Research Letter

Theoretical Study of Sequence Selectivity and Preferred Binding Mode of Psoralen with DNA

1Department of Natural Sciences and Örebro Life Science Center, Örebro University, Örebro 701 82, Sweden
2Faculty of Chemistry, University of Uruguay (UdelaR), Montevideo 11800, Uruguay
3Faculty of Pharmacy, University of Lisbon, a. Prof. Gama Pinto Avenue, Lisbon 1649-019, Portugal

Received 11 July 2007; Accepted 10 October 2007

Academic Editor: L. Serrano-Andrés

Copyright © 2007 Patricia Saenz-Méndez et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand. We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5-TpA in (AT)n sequences.