Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities

Increase in affinity with incubation time for ligands with polyfluorophenyl imido-N extensions. Affinity as a function of incubation time in the dark for (A) SPN2 with a variety of DFHBI derivatives in buffers identified in the legend and (B) Broccoli in buffer SB. (C) Data from A represented as a semi-log plot. (D) BRC was incubated for 18 h with PFP-DFHBI in buffer SB (18 h pre-melt), then melted at 80°C for 5 min, shifted to 23°C and the affinity measured after 10 min, 18 and 36 h post-melt. (E) The influence on the K_a of SPN2 and BRC of increasing numbers of fluorines on the phenyl extension.