Database proton NMR chemical shifts for RNA signal assignment and validation
 

Database proton NMR chemical shifts for RNA signal assignment and validation


Abstract The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the 1H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watsonâ??Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 43 possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA 1H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

• Content Type Journal Article
• Category Article
• Pages 1-14
• DOI 10.1007/s10858-012-9683-9
• Authors
  • Shawn Barton, Howard Hughes Medical Institute, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
  • Xiao Heng, Howard Hughes Medical Institute, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
  • Bruce A. Johnson, Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
  • Michael F. Summers, Howard Hughes Medical Institute, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738

Source: Journal of Biomolecular NMR