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Nucleic Acids Research, 2001, Vol. 29, No. 4 936-942
© 2001 Oxford University Press

Structural analysis of the binding modes of minor groove ligands comprised of disubstituted benzenes

Cheryl A. Hawkins1, Charles Watson2, Yinfa Yan3, Bing Gong3 and David E. Wemmer1,2,*

1Department of Chemistry and 2Graduate Group in Biophysics, University of California, Berkeley, CA 94720-1460, USA and 3Department of Chemistry, University of Toledo, Toledo, OH 43606-3390, USA

Two-dimensional homonuclear NMR was used to characterize synthetic DNA minor groove-binding ligands in complexes with oligonucleotides containing three different A-T binding sites. The three ligands studied have a C2 axis of symmetry and have the same general structural motif of a central para-substituted benzene ring flanked by two meta-substituted rings, giving the molecules a crescent shape. As with other ligands of this shape, specificity seems to arise from a tight fit in the narrow minor groove of the preferred A-T-rich sequences. We found that these ligands slide between binding subsites, behavior attributed to the fact that all of the amide protons in the ligand backbone cannot hydrogen bond to the minor groove simultaneously.

* To whom correspondence should be addressed. Tel: +1 510 486 4318; Fax: +1 510 486 6059; Email: dewemmer{at}lbl.gov Present address: Bing Gong, Department of Chemistry, Natural Sciences Complex, State University of New York, Buffalo, NY 14260, USA


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