Biomolecular NMR Spectroscopy of Ribonucleic Acids

Thorsten Dieckmann, University of Waterloo, Waterloo, Ontario, Canada
Pascale Legault, Université de Montréal, Montréal, Quebec, Canada

Published online: May 2008

DOI: 10.1002/9780470015902.a0021033

Biomolecular nuclear magnetic resonance (NMR) spectroscopy allows the characterization of structural and dynamic properties of ribonucleic acids (RNAs) in solution. The NMR-based determination of high-resolution three-dimensional (3D) structures has been achieved for RNAs up to ca. 100 nucleotides. Biomolecular NMR also provides valuable information about RNA–ligand interactions and the role of metal ions and shifted pKa in RNA structure and catalysis.

Keywords: RNA structure; isotope labelling; molecular dynamics; metal ion binding

Figure 1. Diagram outlining the protocol for preparation of an NMR sample of RNA.
Figure 2. Diagram describing the stepwise procedure for solution structure determination of RNA by NMR spectroscopy.
Figure 3. Resonance assignment of imino protons based on the secondary structure of the RNA. (a) G and U imino protons stabilized by the formation of Watson–Crick U–A and G–C base pairs give strong NOE signals to specific atoms of the paired residue (pink lines) that allow their identification. (b) Secondary structure of the SLV (stem-loop V) RNA derived from the Neurospora VS (Varkud satellite) ribozyme (Campbell and Legault, 2005) outlining the nuclear Overhauser enhancement (NOE) connectivities between imino protons of adjacent base pairs in the secondary structure (pink lines). (c) Imino region of the 2D nuclear Overhauser enhancement spectroscopy (NOESY) spectrum of SLV showing the path of NOE connectivities (pink lines) between imino protons of adjacent base pairs. The imino protons of the two base pairs at the end of the stem (G1-C17 and U6-A12) are not observed in this spectrum due to the dynamics of these base pairs.
Figure 4. Sequential assignment of nonexchangeable protons in RNA. (a) Secondary structure of the SLI¢ (stem-loop I) RNA derived from the Neurospora VS ribozyme (Hoffmann et al., 2003). (b) Dinucleotide fragment (C4-G5) extracted from the 3D structure of SLI¢ (PDB entry: 1OW9) showing the short intra- and internucleotide H6/H8-H1¢ distances (pink dotted lines). (c) Region of the 2D NOESY spectrum of SLI¢ showing the path of NOE connectivities (pink lines) for the sequential walk between residues 4 and 11 (see text). The intranucleotide H6/H8-H1¢ NOE signals are annotated by the residue numbers.
Figure 5. (a) Ribose structure and ribose proton nomenclature. (b) Ribose region of the 2D 1H–13C correlation spectrum of SLI¢ showing the increased signal resolution provided by the 13C chemical shift.
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 Further Reading
    Flinders J and Dieckmann T (2006) NMR spectroscopy of ribonucleic acids. Progress in Nuclear Magnetic Resonance Spectroscopy 48: 137–159.
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Related Sub-Topics:

Nucleic Acid Structure | Nuclear Magnetic Resonance | RNA Structure and Function | Biochemical and Biophysical Techniques | Nucleic Acids: Structure, Function, Metabolism
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Article Title: Biomolecular NMR Spectroscopy of Ribonucleic Acids
 
How to Cite close
Dieckmann, Thorsten, and Legault, Pascale(May 2008) Biomolecular NMR Spectroscopy of Ribonucleic Acids. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021033]