Extended Data Fig. 5: LOGO analyses for preferred and discriminated sequences for C14 – C20.

Left, LOGO analysis of the selected RNAs in the top 0.5% of Z_obs and the secondary structures of the selected RNAs with the four highest Z_obs values for compounds C14–C20. Generally, these compounds prefer motifs rich in C and A residues, with position 6 almost exclusively A. Similar to C1–C6, 3×3 internal loops predominate for C7–C20 (75%) (p < 0.001, as compared to its distribution in 3×3 ILL), with single nucleotide bulges and 1×1 and 2×2 internal loops comprising 14%. Right, LOGO analysis of RNAs discriminated against by each small molecule, i.e., in the bottom 0.5% of Z_obs, and the secondary structures of the RNAs discriminated against with the four lowest Z_obs values for compounds C1–C20. Preferred sequences for C14–C20 are rich in C and A, with positions 1 and 6 preferred as G and A, respectively. Two of the azoliums, C16 and C17, are the most similar to C1; in C16, the substituted phenyls in C1 are replaced with methyl groups, while in C17, the alkyl chains have been shortened from C₁₅ to C₇ and the 1,3-diisopropyl-2-methyphenyl groups have been replaced with benzyl groups. Like the other azolium salts, LOGO analyses of these three compounds revealed a preference for C and A nucleotides, with positional differences for all three molecules.