Two-dimensional1h and31p nmr spectra of a decamer oligodeoxyribonucleotide duplex and a quinoxaline ([mecys3, mecys7]tandem) drug duplex complex

Robert Powers, Richard K. Olsen, David G. Gorenstein

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20 Scopus citations


Assignment of the1H and3IP NMR spectra of a decamer oligodeoxyribonucleotide duplex, d(CCCGATCGGG), and its quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex has been made by two-dimensional1H-1H and heteronuclear3IP-1H correlated spectroscopy. The3IP chemical shifts of this 10 base pair oligonucleotide follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the31P resonance occurs. While the31P chemical shifts show sequence-specific variations, they also do not generally follow the Calladine “rules” previously demonstrated.31P NMR also provides a convenient monitor of the phosphate ester backbone conformational changes upon binding of the drug to the duplex. Although the quinoxaline drug, [MeCys3, MeCys7] TANDEM, is generally expected to bind to duplex DNA by bis-intercalation, only small31P chemical shift changes are observed upon binding the drug to duplex d(CCCGATCGGG). Additionally, only small perturbations in the1H NMR and UV spectra are observed upon binding the drug to the decamer, although association of the drug stabilizes the duplex form relative to the other states. These results are consistent with a non-intercalative mode of association of the dmg. Modeling and molecular mechanics energy minimization demonstrate that a novel structure in which the two quinoxaline rings of the drug binds in the minor groove of the duplex is possible.

Original languageEnglish (US)
Pages (from-to)515-556
Number of pages42
JournalJournal of Biomolecular Structure and Dynamics
Issue number3
StatePublished - Dec 1989
Externally publishedYes

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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