Theoretical prediction of binding modes and hot sequences for allopsoralen–DNA interaction
Molecular docking studies of two duplex DNA sequences as target fragments and allopsoralen as ligand were performed. The calculated interaction energies showed that the ligand can be docked into the minor groove as well as become intercalated. However, unlike psoralen, allopsoralen preferred binding mode for non-poly-TA sequences is minor groove binding. Calculated energies for intercalation between different base pairs suggest that the predicted sequence selectivity for allopsoralen is analogous to that observed for psoralen. Intercalation is favored in 5′-TpA sites in poly-TA sequences.
Patricia Saenz Méndeza#, Rita C. Guedes*, Daniel J.V.A. dos Santos*, Leif A. Eriksson#
# Department of Natural Sciences and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
* Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-019 Lisbon, Portugal
http://dx.doi.org/10.1016/j.cplett.2007.10.105