Journal of the American Chemical Society, Vol.132, No.30, 10318-10329, 2010
Quantitative 2D and 3D Gamma-HCP Experiments for the Determination of the Angles alpha and zeta in the Phosphodiester Backbone of Oligonucleotides
The quantitative Gamma-(HCP) experiment, a novel heteronuclear NMR pulse sequence for the determination of the RNA backbone angles alpha(O3'(i-1)-P-i-O5'(i)-C5'(i)) and zeta(C3'(i)-O3'(i)-Pi+1-O5'(i+1)) in C-13-labeled RNA, is introduced. The experiment relies on the interaction between the CH bond vector dipole and the P-31 chemical shift anisotropy (CSA), which affects the relaxation of the C-13,P-31 double- and zero-quantum coherence and thus the intensity of the detectable magnetization. With the new pulse sequence, five different cross-correlated relaxation rates along the phosphodiester backbone can be measured in a quantitative manner, allowing projection-angle and torsion-angle restraints for the two backbone angles zeta and to be extracted. Two versions of the pulse sequence optimized for the CH and CH2 groups are introduced and demonstrated for a 14-mer cUUCGg tetraloop RNA model system and for a 27-mer RNA with a previously unknown structure. The restraints were incorporated into the calculation of a very high resolution structure of the RNA model system (Nozinovic, S.; et al. Nucleic Acids Res. 2010, 38, 683). Comparison with the X-ray structure of the cUUCGg tetraloop confirmed the high quality of the data, suggesting that the method can significantly improve the quality of RNA structure determination.