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.

The high level of disorder and motional coupling in the ssRNA prevents quantitative analysis of relaxation data using the model-free formalism, which assumes that internal and overall motions are decoupled from one another (51) . This makes it difficult if not impossible to assess the absolute level of disorder in the ssRNA; one can only make qualitative assessments about the relative disorder across different residues. However, it is noteworthy that even the comparatively high R 2 /R 1 values measured in the rigid core ($2.9, Figure 2C ) remain significantly lower than values predicted for a perfectly rigid helical ssRNA ($6.4, Supplementary Figure S4 ) as estimated using the program HYDRONMR (41, 42) . If we assume an overall diffusion tensor predicted by HYDRONMR, we find that central polyadenine residues are highly flexible with an estimated average NMR spin relaxation order parameter S 2 of $0.45 ( Figure 2C and Supplementary Figure S4) . Interestingly, similar though slightly smaller absolute S 2 values are calculated from the REMD simulations (on average S 2 $ 0.36 for core residues, Figure 2D ). These data indicate that despite measurable stacking interactions and a helical-like average conformation, the polyadenine core is highly disordered with residues experiencing fluctuations on the order of a ±40 cone angle (61) at pico-to nanosecond timescales.