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Org Biomol Chem. 2010 Feb 7;8(3):648-54. doi: 10.1039/b918252g. Epub 2009 Dec 7.

Structural analysis of the binding of the diquaternary pyridophenazine derivative dqdppn to B-DNA oligonucleotides.

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Dept. of Chemistry, University of Sheffield, Brook Hill, Sheffield, S3 7HF, UK.


The interaction of the ethylene-bipyridyldiylium-naphthaphenazine dication, dqdppn, with several hexa- and octanucleotide duplexes has been studied using CD and NMR. Taken together, these studies reveal that with the hexanucleotide, dqdppn intercalates into the terminal base pair, and causes a large twisting of the terminal base pair. In contrast, with all three octanucleotides, dqdppn intercalates more centrally within the sequence. The NMR-derived structures of two of the binding complexes demonstrate that dqdppn intercalates from the major groove in an unusual 'side-on' geometry, rather than threading through the helix. An analysis of these results indicates that the preferred binding site is not sequence-specific, but primarily at the most conformationally flexible DNA step.

[Indexed for MEDLINE]

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