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J Phys Chem B. 2013 Feb 21;117(7):2045-52. doi: 10.1021/jp310863c. Epub 2013 Feb 7.

Utility of 1H NMR chemical shifts in determining RNA structure and dynamics.

Author information

1
Department of Chemistry, University of California Irvine 1102 Natural Sciences 2, Irvine, California 92697, USA.

Abstract

The development of methods for predicting NMR chemical shifts with high accuracy and speed is increasingly allowing use of these abundant, readily accessible measurements in determining the structure and dynamics of proteins. For nucleic acids, however, despite the availability of semiempirical methods for predicting (1)H chemical shifts, their use in determining the structure and dynamics has not yet been examined. Here, we show that (1)H chemical shifts offer powerful restraints for RNA structure determination, allowing discrimination of native structure from non-native states to within 2-4 Å, and <3 Å when highly flexible residues are ignored. Theoretical simulations shows that although (1)H chemical shifts can provide valuable information for constructing RNA dynamic ensembles, large uncertainties in the chemical shift predictions and inherent degeneracies lead to higher uncertainties as compared to residual dipolar couplings.

PMID:
23320790
PMCID:
PMC3676946
DOI:
10.1021/jp310863c
[Indexed for MEDLINE]
Free PMC Article

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