A suite of 2H NMR spin relaxation experiments for the measurement of RNA dynamics

A suite of H-2-based spin relaxation NMR experiments is presented for the measurement of molecular dynamics in a site-specific manner in uniformly C-13, randomly fractionally deuterated (similar to 50%) RNA molecules. The experiments quantify H-2 R-1 and R-2 relaxation rates that can subsequently be analyzed to obtain information about dynamics on a pico- to nanosecond time scale. Sensitivity permitting, the consistency of the delta can be evaluated by measuring all five rates that are accessible for a spin 1 particle and establishing that the rates obey relations that are predicted from theory. The utility of the methodology is demonstrated with studies of the dynamics of a 14-mer RNA containing the UUCG tetraloop at temperatures of 25 and 5 degrees C. The high quality of the data, even at 5 degrees C, suggests that the experiments will be of use for the study of RNA molecules that are as large as 30 nucleoticles.