Figure 6.

Dynamic model for theophylline- and 3MX-binding aptamers that illustrates the transition from an ensemble of conformations in free RNA to complexes. The black and blue colors of base P27 indicate dark and bright fluorescent states, respectively. The percentages indicate the relative populations of each different states for base 27 in the free RNA, two are identified as inactive, one as active. The dynamic nature of the base 27 in one of the inactive state is represented by the blurred black boxes. The differences in the conformational distribution of the complex state between the theophylline- and 3MX-binding aptamers are indicated in the conformational ensemble of complex. Curved arrows indicate some undefined interactions between P27 and the aptamers in the complex state.