Fig. 6: Reactivity profiles of generated aptamers with chemical probing.
From: Designing molecular RNA switches with Restricted Boltzmann machines
Black triangles refer to highlighted key sites, see Fig. 5. A, B SHAPE reactivity and differential reactivity profiles for one RBM-generated aptamer with RBM score 321.41. C, D Same as (A, B) for one RBM-generated aptamer with RBM score 357.79. E Average differential reactivities in response to SAM of 54 RBM generated sequences with high RBM scores (>300) (blue), across the 108 sites of the alignment. For comparison, the average differential reactivities for 204 natural sequences are shown in the background (gray). High-RBM score sequences recapitulate protection of sites involved in the structural switch in response to SAM binding (highlighted in green). F Average differential reactivities in response to SAM of rCM generated sequences (red). Natural sequences are shown in background for comparison. rCM sequences fail to recapitulate the expected protections associated to the structural switch (red arrows). In both (E, F), the thickness of the bands indicates the standard deviation. The correlations between the site-dependent differential reactivities are 0.84 between Natural and RBM (score > 300) (E) and 0.18 between Natural and rCM (F) with an empirical bootstrap p < 10−6, see Supplementary Fig. S24.
