Quantitative Γ-HCNCH: determination of the glycosidic torsion angle χ in RNA oligonucleotides from the analysis of CH dipolar cross-correlated relaxation by solution NMR spectroscopy

A novel NMR pulse sequence is introduced to determine the glycosidic torsion angle χ in 13C,15N-labeled oligonucleotides. The quantitative Γ-HCNCH measures the dipolar cross-correlated relaxation rates \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Gamma_{{\rm C6H6,C1}^{\prime}{\rm H1}^{\prime}}^{\rm DD,DD}$$\end{document} (pyrimidines) and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Gamma_{{\rm C8H8,C1}^{\prime}{\rm H1}^{\prime}}^{\rm DD,DD}$$\end{document} (purines). Cross-correlated relaxation rates of a 13C,15N-labeled RNA 14mer containing a cUUCGg tetraloop were determined and yielded χ-angles that agreed remarkably well with data derived from the X-ray structure of the tetraloop. In addition, the method was applied to the larger stemloop D (SLD) subdomain of the Coxsackievirus B3 cloverleaf 30mer RNA and the effect of anisotropic rotational motion was examined for this molecule. It could be shown that the χ-angle determination especially for nucleotides in the anti conformation was very accurate and the method was ideally suited to distinguish between the syn and the anti-conformation of all four types of nucleotides.