Assignment Strategies and Analysis of Cross-Peak Patterns and Intensities in the Three-Dimensional Homonuclear TOCSY-NOESY of RNA

Abstract

The application of 3D TOCSY-NOESY to the analysis of RNA is presented, using a TOCSY-NOESY spectrum of the RNA duplex r(5′GGGCUGAAGCCU′). It is shown that for RNA molecules, 3D spectra can be obtained with a digital resolution comparable to that obtained for 2D NMR with full spectral information. The improvement in assignment over 2D methods is shown and discussed on the basis of an assignment strategy presented earlier. A simple and straightforward method for determining sugar puckers and γ backbone torsion angles is presented, which is derived from an analysis of cross-peak intensities originating from the TOCSY coherence transfer among sugar protons and HS′/5″ protons. The stereospecific assignment of the HS′/5″ resonances in 3D TOCSY-NOESY spectra is also discussed.