Fig. 6
ACE-Scan of the adenine-binding add riboswitch aptamer. a Secondary structure of the apoB (left) and apoA (right) states of the add riboswitch aptamer46. Stems (P1–P5), loops (L2, L3) and junctions (J1–2, J2–3, and J3–1) are labeled. The location of adenine binding and other functional regions present in the holo structure are shown superimposed on the apoA state as follows: the kissing interaction between L2 and L3 (dotted lines), nucleotides known to interface with adenine (green bases and green dashed lines), and pairs of nucleotides known to interface in the holo state (black dashed lines). Riboswitch elements 3ʹ of the aptamer involved in translational control were not synthesized here and are drawn schematically as black and red lines. Bases outside the consensus aptamer sequence are colored gray. b–d Heat maps showing the (b) hybridization landscape of add DAs at 23 °C, (c) koff landscape of add DAs at 23 °C under 12 mM Mg2+ buffer-only conditions, and (d) k*off,4 mM landscape of add DAs subject to 4 mM adenine, revealing induced fit binding
