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Nucleic Acids Research, 2003, Vol. 31, No. 17 5084-5089
© 2003 Oxford University Press

Determination of DNA minor groove width in distamycin-DNA complexes by solid-state NMR

Greg L. Olsen, Elizabeth A. Louie, Gary P. Drobny and Snorri Th. Sigurdsson*

Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA

*To whom correspondence should be addressed. Tel: +1 206 616 8276; Fax: +1 206 685 8665; Email: sigurdsson{at}chem.washington.edu

We have performed solid-state 31P-19F REDOR nuclear magnetic resonance (NMR) experiments to monitor changes in minor groove width of the oligonucleotide d(CGCAAA2'FUTGGC)·d(GCCAAT(pS)TT GCG) (A3T2) upon binding of the drug distamycin A at different stoichiometries. In the hydrated solid-state sample, the minor groove width for the unbound DNA, measured as the 2'FU7–pS19 inter-label distance, was 9.4 ± 0.7 Å, comparable to that found for similar A:T-rich DNAs. Binding of a single drug molecule is observed to cause a 2.4 Å decrease in groove width. Subsequent addition of a second drug molecule results in a larger conformational change, expanding this minor groove width to 13.6 Å, consistent with the results of a previous solution NMR study of the 2:1 complex. These 31P-19F REDOR results demonstrate the ability of solid-state NMR to measure distances of 7–14 Å in DNA–drug complexes and provide the first example of a direct spectroscopic measurement of minor groove width in nucleic acids.


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