Format

Send to

Choose Destination
Sci Rep. 2017 Jul 14;7(1):5393. doi: 10.1038/s41598-017-05821-z.

RNA structure refinement using NMR solvent accessibility data.

Author information

1
Center for Integrated Protein Science Munich, Department Chemie, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.
2
Institute of Structural Biology, Helmholtz Zentrum München, Ingolstadter Landstr. 1, 85764, Neuherberg, Germany.
3
Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Germany.
4
Center for Integrated Protein Science Munich, Department Chemie, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany. tobias.madl@medunigraz.at.
5
Institute of Structural Biology, Helmholtz Zentrum München, Ingolstadter Landstr. 1, 85764, Neuherberg, Germany. tobias.madl@medunigraz.at.
6
Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz, Harrachgasse 21, 8010, Graz, Austria. tobias.madl@medunigraz.at.

Abstract

NMR spectroscopy is a powerful technique to study ribonucleic acids (RNAs) which are key players in a plethora of cellular processes. Although the NMR toolbox for structural studies of RNAs expanded during the last decades, they often remain challenging. Here, we show that solvent paramagnetic relaxation enhancements (sPRE) induced by the soluble, paramagnetic compound Gd(DTPA-BMA) provide a quantitative measure for RNA solvent accessibility and encode distance-to-surface information that correlates well with RNA structure and improves accuracy and convergence of RNA structure determination. Moreover, we show that sPRE data can be easily obtained for RNAs with any isotope labeling scheme and is advantageous regarding sample preparation, stability and recovery. sPRE data show a large dynamic range and reflect the global fold of the RNA suggesting that they are well suited to identify interaction surfaces, to score structural models and as restraints in RNA structure determination.

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center