Anisotropic rotation in nucleic acid fragments: significance for determination of structures from NMR data

Proton-proton relaxation rate constants depend on the angle between the internuclear vector and the principal axis of rotation in symmetric top molecules. It is possible to determine to rotational correlation times of the equivalent ellipsoid for DNA fragments from a knowledge of the axial ratio and the cross-relaxation rate constant for the cytosine H6-H5 vectors. The cross-relaxation rate constants for the cytosine H6-H5 vectors have been measured in the 14-base-pair sequence dGCTGTTGACAATTA.dTAATTGTCAACAGC at four temperatures. The results, along with literature data for DNA fragments ranging from 6 to 20 base pairs can be accounted for by a simple hydrodynamic equation based on the formalism of Woessner (1962). The measured cross-relaxation rate constant is independent of position in the sequence and is consistent with the absence of large amplitude internal motions on the Larmor time scale. All the data can be described by a simple hydrodynamic model, which accounts for the rotational anisotropy of the DNA fragments and allows the correlation time for end-over-end tumbling to be determined if the approximate rise per base pair is known. This is the correlation time that dominates the spectral density functions for internucleotide vectors and is significantly different from that calculated for a sphere of the same hydrodynamic volume for fragments containing more than about 14 base pairs. This method therefore allows NOE intensities used for structure calculation of nucleic acids to be treated more rigorously.