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. Author manuscript; available in PMC: 2020 Jul 24.
Published in final edited form as: J Am Chem Soc. 2019 Dec 31;142(2):907–921. doi: 10.1021/jacs.9b10535

Figure 2.

Figure 2.

Evidence for bulge-dependent secondary binding site in the TAR upper helix. (A) Comparison of secondary structures of the TAR and the bulgeless mutant in the absence of ligand. Resonances colored in yellow correspond to the putative secondary binding site. (B) CSPs as a function of ARG concentration and temperature for residues that are sensitive to the bulge-dependent secondary binding site on TAR that is abolished in the bulgeless mutant. Color coding of temperatures follows that of Figure 1C. The data supports that the secondary binding site is localized to the upper helix region between residues A27 and G36. The curved trajectories seen for A27-C8 and G28-C8 in TAR indicate they are sensitive to both the α and β sites. This is consistent with previous results that the α site ARG is stacked above A22 and contacts G26 just below A27. Note that the chemical shifts for G36-C1′ and G36-C8 in TAR are only sensitive to the β site ligand.