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

Elizabeth A. Louie, Panadda Chirakul, Vinodhkumar Raghunathan, Snorri Th Sigurdsson, Gary P. Drobny

Rannsóknarafurð: Framlag til fræðitímaritsGreinritrýni


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 Å. 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.

Upprunalegt tungumálEnska
Síður (frá-til)11-24
FræðitímaritJournal of Magnetic Resonance
Númer tölublaðs1
ÚtgáfustaðaÚtgefið - jan. 2006


Funding Information:
We thank M.E. Merritt for helpful discussions; J. Schaefer and his group members for P–CF 3 REDOR simulations, helpful discussions, and comments; T.E. Edwards, J. D. Wellhausen, J. C. Markley, and D. Sologub for synthesizing and purifying the DNA; N.A. Oyler for the use of his Matlab code for the NMR data workup and the C++ code for the P–F REDOR simulations; and James Gibson for reading repeated revisions of the manuscript. This research was supported by the National Institute of Health. Grants (RO1 EB03152-O5) and (RO1 DE-12554-08) and by NSF Grant (DMR 0110505).


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