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Theoretical prediction of binding modes and hot sequences for allopsoralen–DNA interaction

Authors
Journal
Chemical Physics Letters
0009-2614
Publisher
Elsevier
Publication Date
Volume
450
Identifiers
DOI: 10.1016/j.cplett.2007.10.105

Abstract

Abstract 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.

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