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Using solid-state 31P{19F} REDOR NMR to measure distances between a trifluoromethyl group and a phosphodiester in nucleic acids.

Louie EA, Chirakul P, Raghunathan V, Sigurdsson ST, Drobny GP

University of Washington, Chemistry Department, Campus Box 351700, Seattle, WA 98195-1700, USA.

REDOR is a solid-state NMR technique frequently applied to biological structure problems. Through incorporation of phosphorothioate groups in the nucleic acid backbone and mono-fluorinated nucleotides, 31P{19F} REDOR has been used to study the binding of DNA to drugs and RNA to proteins through the detection of internuclear distances as large as 13-14 A. In this work, 31P{19F} REDOR is further refined for use in nucleic acids by the combined use of selective placement of phosphorothioate groups and the introduction of nucleotides containing trifluoromethyl (-CF3) groups. To ascertain the REDOR-detectable distance limit between an unique phosphorous spin and a trifluoromethyl group and to assess interference from intermolecular couplings, a series of model compounds and DNA dodecamers were synthesized each containing a unique phosphorous label and trifluoromethyl group or a single 19F nucleus. The dipolar coupling constants of the various 31P and 19F or -CF3 containing compounds were compared using experimental and theoretical dephasing curves involving several models for intermolecular interactions.

Published 12 December 2005 in J Magn Reson, 178(1): 11-24.
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