FIGURE 7.

Solvent exposure of the VCI-II tandem aptamer probed by hydroxyl radical cleavage as a function of Mg²⁺ concentration in the absence (A) and presence (B) of 10 mM glycine, both with a 2 M NaCl background. Data are for residues 47–150 and were normalized such that the amount of cleavage at 0 mM Mg²⁺ corresponds to zero (for each of the titration sets). Blue regions show increasing protections from cleavage, and red regions show increasing cleavage. In the presence of glycine (B), protections increase for certain regions, while no protections were increased when no glycine was added (A). This observation gives further evidence that the M state is populated in 2 M NaCl. For comparison, relative protections determined from a glycine titration in 10 mM Mg²⁺ background are shown (far right). The data in this reference lane are normalized to 10 mM Mg²⁺ and no glycine, and are taken from Lipfert et al. (2007b). This glycine titration in the 10 mM Mg²⁺ background probes the M-to-B transition, and hence, can be directly compared with both A and B, where the M state is populated in 2 M NaCl. This same M-to-B transition is observed in B.