Database proton NMR chemical shifts for RNA signal assignment and validation |
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Authors: | Shawn?Barton Xiao?Heng Email author" target="_blank">Bruce?A?JohnsonEmail author Email author" target="_blank">Michael?F?SummersEmail author |
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Institution: | 1.Howard Hughes Medical Institute,University of Maryland, Baltimore County,Baltimore,USA;2.Department of Chemistry and Biochemistry,University of Maryland, Baltimore County,Baltimore,USA;3.One Moon Scientific, Inc.,Westfield,USA |
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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 Watson–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. |
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