Determination of fast dynamics of nucleic acids by NMR

Double-stranded oligonucleotides of <10 base pairs are adequately described as an isotropic rotor, using the correlation time for the cytosine H6-H5 vector. For longer fragments, the cylindrical model should be used for detailed analysis of NOEs. The appropriate correlation times can be calculated using the formulae of Tirado and Garcia de la Torre 32 or derived from measurements of the cross-relaxation rate constants for cytosine (or uridine) H6-HS. Order parameters describing the degree of motion of different vectors on the subnanosecond time scale vary substantially, with typical values of S 2 > 0.8 for base vectors and 0.5-0.8 for intrasugar and base-sugar vectors. Order parameters for terminal nucleotides are typically significantly smaller than for internal nueleotides, which may also mean that their conformation will be less well determined in the formalism of a unique structure. The CSA relaxation rates of the phosphodiesters appear to be insensitive to internal motions and may, therefore, provide the most accurate estimate of the overall tumbling time in nucleic acid fragments. Using a combination of relaxation data for different nuclei and different spectrometer frequencies may be expected to yield detailed information about fast motions in nucleic acid fragments.