Extended Data Fig. 2: LOGO analyses for C1 – C6, showing both preferred and discriminated sequences and structures.
From: Programming inactive RNA-binding small molecules into bioactive degraders
a, LOGO analysis of the selected RNAs in the top 0.5% of Zobs and the secondary structures of the selected RNAs with the four highest Zobs values. b, LOGO analysis of RNAs discriminated against by each small molecule, i.e., in the bottom 0.5% of Zobs, and the secondary structures of the RNAs discriminated against with the four lowest Zobs values. Interestingly, many have GC closing base pairs and are 2×2 nucleotide internal loops. Similarities and differences were found amongst the small molecules. For example, within the azolium scaffold, C1 prefers C at positions one and three and A at positions four and six (that is, internal loops with two Cs opposite two As), while C3, which differs by the substituents on the azolium core, prefers A at positions one, three and four, but C at positions six. Interestingly, C1–C6, despite their chemical differences in scaffolds, all discriminate against a 5’ GC closing base pair (G and C at positions one and six, respectively).
