Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

Eichhorn, Catherine D.; Feng, Jun; Suddala, Krishna C.; Walter, Nils G.; Brooks, Charles L.; Al-Hashimi, Hashim M.

In general, isotropic motions tend to reduce the observed RDC value, approaching zero at the limit of spatially unrestricted isotropic motions (61, 64, 65) . In the ssRNA, large base C-H RDCs are measured in the polyadenine tract residues that gradually decrease at the termini ( Figure 3A ). Although small RDC values can also arise from static placement of the bond vector near the magic angle relative to the principal direction of order, the overall trends observed are consistent with NMR chemical shift and S 2 rel data suggesting that the RDCs indicate increased dynamic averaging at the termini ( Figure 3A) . Interestingly, the near-zero RDCs measured at terminal residues ( Figure 3A and Supplementary Figure S5 ) agree more closely to the REMD simulations compared to the S 2 rel values, indicating that the discrepancy between the measured and computed S 2 rel values may be due to truncation of the S 2 sensitivity to motions faster than nanoseconds. These results add to a growing number of NMR studies on different types of RNA showing that RDC data are capable of probing motions that are incompletely sensed by spin relaxation due to truncation of the time-sensitivity by overall correlation time of the molecule (64, (66) (67) (68) . Unfortunately, severe spectral overlap, particularly pronounced in the Pf1 phage sample, prevented measurement of several C1 0 H1 0 RDCs for the polyadenine core.