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

Patricia Saenz Méndez, Rita C. Guedes, Daniel J.V.A. dos Santos, Leif A. Eriksson

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)127-131
Number of pages5
JournalChemical Physics Letters
Volume450
Issue number1-3
DOIs
Publication statusPublished - 14 Dec 2007
Externally publishedYes

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