Table 2.

Sequences used in in vivo flow cytometry analysis. Italic sequences indicates the tRNA scaffold that is appended onto the terminal ends. Bold sequences indicate the Spinach2 sequence, which flanks the riboswitch sequence. Italic and underlined indicate the part of the transducer stem derived from the native riboswitch. Blue indicates the tetraloop used for circular permutation of the P1 stem in the riboswitch. Red indicates the site of mutation(s) that abolish ligand binding to the aptamer.

Name	Sequence (5’ to 3’)
Spinach2	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCAGTAGGCTGCTTCGGCAGCCTACTTGTTGAGTAGAGTGTGAGCTCCGTAAC TAGTTACATCCGGCCGCGGGTCCAGGGTTCAAGTCCCTGTTCGGGCGCCA
Spinach2 Mutant	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGccTCCAGTAGGCTGCTTCGGCAGCCTACTTGTTGAGTAGAGTGTGAGCTCCGTAACT AGTTACATCCGGCCGCGGGTCCAGGGTTCAAGTCCCTGTTCGGGCGCCA
Tt 1–4	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCATATCAAGAGAGGTGGAGGGACTGGCCCGATGAAACCCGGCAACCAGCCTTAG GGCATGGTGCCAATTCCTGCAGCGGTTTCGCTGAAAGATGTTGTTGAGTAGAGTGTGAGCT CCGTAACTAGTTACATCCGGCCGCGGGTCCAGGGTTCAAGTCCCTGTTCGGGCGCCA
Tt 1–4 Mutant	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCATATCAgaAGAGGTGGAGGGACTGGCCCGATGAAACCCGGCAACCAGCCTTAG GGCATGGTGCCAATTCCTGCAGCGGTTTCGCTGAAAGATGTTGTTGAGTAGAGTGTGAGCT CCGTAACTAGTTACATCCGGCCGCGGGTCCAGGGTTCAAGTCCCTGTTCGGGCGCCA
Bc 1–5	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCACTTATAACGAGAAGCGGAGGGACTGGCCCAATGAAGCTTCAGCAACCATTCAT TGCGATGAAAAGGTGCTAAATCCAGCAAAGGGAACTTTGGCAGATAAGTTGTTGAGTAGAG TGTGAGCTCCGTAACTAGTTACATCCGGCCGCGGGTCCAGGGTTCAAGTCCCTGTTCGGG CGCCA
Bc 1–5 Mutant	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCACTTATAAgcAGAAGCGGAGGGACTGGCCCAATGAAGCTTCAGCAACCATTCAT TGCGATGAAAAGGTGCTAAATCCAGCAAAGGGAACTTTGGCAGATAAGTTGTTGAGTAGAG TGTGAGCTCCGTAACTAGTTACATCCGGCCGCGGGTCCAGGGTTCAAGTCCCTGTTCGGG CGCCA
Bs 4-4	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCAGCTTGGAAGATAAGAAGCAATTCTTATCAAGAGAAGCAGAGGGACTGGCCCG ACGAAGCTTCAGCAACCGGTGTAATGGCGATCAGCCATGACCAAGGTGCTAAATCCAGCAAG CTTGTTGAGTAGAGTGTGAGCTCCGTAACTAGTTACATCCGGCCGCGGGTCCAGGGTTC AAGTCCCTGTTCGGGCGCCA
Bs 4-4 Mutant	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCAGCTTGGAAGATAAGAAGCAATTCTTATCAgaAGAAGCAGAGGGACTGGCCCG ACGAAGCTTCAGCAACCGGTGTAATGGCGATCAGCCATGACCAAGGTGCTAAATCCAGCAAG CTTGTTGAGTAGAGTGTGAGCTCCGTAACTAGTTACATCCGGCCGCGGGTCCAGGGTTC AAGTCCCTGTTCGGGCGCCA
Bc 4–5	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCACTTTGGCAGATAAGGGGCAACTCTTATAACGAGAAGCGGAGGGACTGGCCCA ATGAAGCTTCAGCAACCATTCATTGCGATGAAAAGGTGCTAAATCCAGCAAAGTTGTTGAGT AGAGTGTGAGCTCCGTAACTAGTTACATC
Bc 4–5 Mutant	GCCCGGATAGCTCAGTCGGTAGAGCAGCGGCCGGATGTAACTGAATGAAATGGTGAAGG ACGGGTCCACTTTGGCAGATAAGGGGCAACTCTTATAAgcAGAAGCGGAGGGACTGGCCCA ATGAAGCTTCAGCAACCATTCATTGCGATGAAAAGGTGCTAAATCCAGCAAAGTTGTTGAGT AGAGTGTGAGCTCCGTAACTAGTTACATC