FIGURE 5.

Melting profiles for several nucleotides in the aptamer domain. (A) Reactivity profile for nucleotide G37, which resides in loop 2 in the absence (triangles) and presence (circles) of hypoxanthine. The dashed line represents the best fit to a model describing a two-state transition. (B) Reactivity profile for U51, a nucleotide in J2/3. The data for reactivity in the absence of ligand (triangles) showed no transition, so they are not fit to a curve. (C) Expanded view of data in panel B. Note that at high temperatures there is a pronounced drop in reactivity; the impact of this effect was reduced with a rolling weighting function to accurately quantify the transition.