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

摘要

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 P-31{F-19} 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 angstrom. In this work, P-31{F-19} 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 REDO R-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 F-19 nucleus. The dipolar coupling constants of the various P-31 and F-19 or -CF3 containing compounds were compared using experimental and theoretical dephasing curves involving several models for intermolecular interactions. (c) 2005 Published by Elsevier Inc.