Fig. 4

Motif detection in a bi-stable fluoride riboswitch. a The accepted structure of the terminated fold, associated with the transcription off state, features three hairpins: P1, P3, and CT (complete terminator). b The accepted structure of the anti-terminated fold, associated with the transcription on state, features a pseudoknot domain (dashed box) and a partial terminator (PT) hairpin. c, d Differential scores between fluoride conditions. Hairpins of loop size 4 and 6 and variable stem size were scored across all possible starting nucleotides of the full-length transcript (100 nt). The x-axis indicates the position of the motif’s start. The y-axis corresponds to hairpins with stems of variable lengths. As sequence constraints were applied, only regions that permit base pairings in the stem were scored. Reds indicate that the motif is more likely in 10 mM NaF, and blues that it is more likely in 0 mM NaF. Dashed lines highlight the location of the P1, P3, and PT/CT hairpins. e Differential scores at the terminator hairpin site as a function of increasing stem size. f, g Pseudoknot scored at each possible starting nucleotide and across all intermediate transcripts without (f) and with (g) fluoride. Reds indicate higher scores. Dashed boxes highlight regions where a pseudoknot is likely present. PK pseudoknot