Utility of 1H NMR Chemical Shifts in Determining RNA Structure and Dynamics

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 H-1 chemical shifts, their use in determining the structure and dynamics has not yet been examined. Here, we show that H-1 chemical shifts offer powerful restraints for RNA structure determination, allowing discrimination of native structure from non-native states to within 2-4 angstrom, and <3 angstrom when highly flexible residues are ignored. Theoretical simulations shows that although H-1 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.