Determination of the Glycosidic Bond Angle χ in RNA from Cross-Correlated Relaxation of CH Dipolar Coupling and N Chemical Shift Anisotropy

Abstract

A new heteronuclear NMR pulse sequence, the quantitative Gamma(HCN) experiment, for the determination of the glycosidic torsion angle chi in (13)C,(15)N-labeled oligonucleotides is described. The Gamma(HCN) experiment allows measurement of CH dipole-dipole, N chemical shift anisotropy cross-correlated relaxation rates (Gamma(C1'H1',N1)(DD,CSA) and Gamma(C2'H2',N9)(DD,CSA) for pyrimidines Gamma(C1'H1'N9)(DD,CSA) and Gamma(C2'H2',N9)(DD,CSA) for purines). A nucleotide-specific parametrization for the dependence of these Gamma-rates on chi based on (15)N chemical shift tensors determined by solid-state NMR experiments on mononucleosides (Stueber, D.; Grant, D. M. J. Am. Chem. Soc. 2002, 124, 10539-10551) is presented. For a 14-mer and a 30-mer RNA of known structures, it is found that the Gamma(HCN) experiment offers a very sensitive parameter for changes in the angle chi and allows restraining of chi with an accuracy of around 10 degrees for residues which do not undergo conformational averaging. Therefore, the Gamma(HCN) experiment can be used for the determination of chi in addition to data derived from (3)J(C,H)-coupling constants. As shown for the 30-mer RNA, the derived torsion angle information can be incorporated as additional restraint, improving RNA structure calculations.