Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements.
Knowledge of (13)C chemical shift anisotropy (CSA) tensors in nucleotide bases is important for interpretation of NMR relaxation data in terms of local dynamic properties of nucleic acids and for analysis of residual chemical shift anisotropy (RCSA) resulting from weak alignment. CSA tensors for protonated nucleic acid base carbons have been derived from measurements on a uniformly (13)C-enriched helical A-form RNA segment and a helical B-form DNA dodecamer at natural (13)C abundance. The magnitudes of the derived CSA principal values are tightly restricted by the magnetic field dependencies of the (13)C transverse relaxation rates, whereas the tensor orientation and asymmetry follow from quantitative measurements of interference between (13)C-{(1)H} dipolar and (13)C CSA relaxation mechanisms. Changes in the chemical shift between the isotropic and aligned states, Deltadelta, complement these measurements and permit cross-validation. The CSA tensors are determined from the experimental Deltadelta values and relaxation rates, under the assumption that the CSA tensor of any specific carbon in a given type of base is independent of the base position in either the RNA or DNA helix. However, the experimental data indicate that for pyrimidine C(6) carbons in A-form RNA the CSA magnitude is considerably larger than in B-form DNA. This result is supported by quantum chemical calculations and is attributed in part to the close proximity between intranucleotide C(6)H and O(5)' atoms in RNA. The magnitudes of the measured CSA tensors, on average, agree better with previous solid-state NMR results obtained on powdered nucleosides than with prior results from quantum chemical calculations on isolated bases, which depend rather strongly on the level of theory at which the calculations are carried out. In contrast, previously computed orientations of the chemical shift tensors agree well with the present experimental results and exhibit less dependence on the level of theory at which the computations are performed.
Ying
Jinfa
J
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Grishaev
Alexander
A
Bryce
David L
DL
Bax
Ad
A
D016880:Anisotropy; D001483:Base Sequence; D002247:Carbon Isotopes; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D050866:Liquid Crystals / Q000737:chemistry*; D008956:Models, Chemical; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D011522:Protons; D011789:Quantum Theory; D012313:RNA / Q000737:chemistry*
D002247:Carbon Isotopes; D011522:Protons; D012313:RNA; D004247:DNA