Figure 5 : Secondary structures and affinities of the selected RNA motif–ligand interactions.

From: Identifying the preferred RNA motifs and chemotypes that interact by probing millions of combinations

Figure 5

The secondary structures shown were predicted by free energy minimization using the RNAstructure program31. The RNA motif–ligand partners that were subjected to binding assays were predicted to have the highest affinities based on analysis by structure-activity relationships through sequencing (StARTS)49,50,51. The red letters in the secondary structures indicate nucleotides that are derived from the randomized region of the libraries; the secondary structure shown is from the boxed nucleotides in Fig. 2. All dissociation constants (Kd) are reported in micromolar. PL-1, HL-1, HL-2 and DL-1 do not bind oligonucleotide 8 (Fig. 2; GAAA tetraloop) or the starting libraries 13 (Kd >200 μM). (a) The RNA motifs selected to bind PL-1. (b) The RNA motifs selected to bind HL-1. (c) The RNA motifs selected to bind DL-1. (d) The RNA motifs selected to bind HL-2. In the RNA identifiers, 'B' indicates a bulge, whereas 'HP' indicates a hairpin. Each experiment was completed in triplicate, and the error bars are the standard deviations.