Using solid-state 31P{19F} REDOR NMR to measure distances between a trifluoromethyl group and a phosphodiester in nucleic acids.
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.
Louie
Elizabeth A
EA
University of Washington, Chemistry Department, Campus Box 351700, Seattle, WA 98195-1700, USA.
Chirakul
Panadda
P
Raghunathan
Vinodhkumar
V
Sigurdsson
Snorri Th
ST
Drobny
Gary P
GP
D018360:Crystallography, X-Ray; D005461:Fluorine / Q000737:chemistry; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009696:Nucleic Acids / Q000737:chemistry*; D010759:Phosphorus Isotopes / Q000737:chemistry
D009696:Nucleic Acids; D010759:Phosphorus Isotopes; D005461:Fluorine