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

Affinities of SPN2 and BRC for imido-N extension ligands. (A) The affinities of SPN2 for compounds of the imido-N extension ligand library in buffer SX (green bars) or buffer IC (yellow bars) after 10 min incubation. (B) The effect of Mg on the affinity of SPN2 for DFHBI. Buffer IC (green bar), buffer IC with 5 mM Mg (yellow bars). (C) The affinities of BRC for some of the imido-N extension ligands in buffer SB (brown bars) or buffer IC (tan bars). All affinities were determined by fluorescence spectroscopy as described in Materials and Methods.