Issue 3, 2010
From the journal:

Organic & Biomolecular Chemistry

Structural analysis of the binding of the diquaternary pyridophenazine derivative dqdppn to B-DNAoligonucleotides†

Philip Waywell,ab   James A. Thomas*a  and  Mike P. Williamson*b  

* Corresponding authors

a Dept. of Chemistry, University of Sheffield, Brook Hill, Sheffield, UK
E-mail: james.thomas@sheffield.ac.uk
Fax: +44 114 222 9346

b Dept. of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, UK
E-mail: m.williamson@sheffield.ac.uk
Fax: +44 114 222 2800

Abstract

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.

Graphical abstract: Structural analysis of the binding of the diquaternary pyridophenazine derivative dqdppn to B-DNA oligonucleotides

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Article information

DOI
https://doi.org/10.1039/B918252G
Article type
Paper
Submitted
03 Sep 2009
Accepted
31 Oct 2009
First published
07 Dec 2009

Org. Biomol. Chem., 2010,8, 648-654

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

P. Waywell, J. A. Thomas and M. P. Williamson, Org. Biomol. Chem., 2010, 8, 648 DOI: 10.1039/B918252G

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