Figure 4.
Analysis of specific and non-specific contacts in CHF-1·RNA recognition. (A) CHF-1 contains residues that potentially engage the RNA Hoogsteen surface along with two solvent exposed lysine residues (K27 and K30). In CHF-2, solvent-exposed cationic residues are replaced with alanine. In CHF-3 residues (R26 and H29) that potentially engage the RNA bases have been substituted with alanine. Models were generated with UCSF ChimeraX using pdb 2zi0. (B) Binding affinities of fluorescein-labeled CHF compounds as determined in a fluorescence polarization assay. Bar graph of affinities represented in log(Ka). (B) Kd values of CHF compounds. nb = no binding observed. N.D. = not determined. (C) Hairpin nucleotide sequences used in the analysis. Error bars represent the standard deviation of three independent experiments.