Rotational diffusion tensor of nucleic acids from 13C NMR relaxation

Rotational diffusion properties have been derived for the DNA dodecamer d(CGCGAATTCGCG)(2) from C-13 R-1rho and R-1 measurements on the C-1', C-3', and C-4' carbons in samples uniformly enriched in C-13. The narrow range of C-H bond vector orientations relative to the DNA axis make the analysis particularly sensitive to small structural deviations. As a result, the R-1rho/R-1 ratios are found to fit poorly to the crystal structures of this dodecamer, but well to a recent solution NMR structure, determined in liquid crystalline media, even though globally the structures are quite similar. A fit of the R-1rho/R-1 ratios to the solution structure is optimal for an axially symmetric rotational diffusion model, with a diffusion anisotropy, D-parallel to/D-perpendicular to, of 2.1+/-0.4, and an overall rotational correlation time, (2D(parallel to) + 4D(perpendicular to))(-1), of 3.35 ns at 35degreesC in D2O, in excellent agreement with values obtained from hydrodynamic modeling.