Table 1.
Sequences of synthetic oligonucleotides
| Code name | Sequence (5’–3’) |
|---|---|
| RNAs | |
| KsgA UM | GUAACCGUAGGGGAACCUGCGGUUGGAUCAC |
| KsgA Me | GUAACCGUAGGGGm62Am62ACCUGCGGUUGGAUCAC |
| RrmA UM | GAACCGACUAAUGUUGAAAAAUUAGCG |
| RrmA Me | GAACCGACUAAUm1GUUGAAAAAUUAGCG |
| RsmE UM | GGGUGAAGUCGUAACAAGGUAACCG |
| RsmE Me | GGGUGAAGUCGm3UAACAAGGUAACCG |
| RlmJ UM | UUGAACUCGCUGUGAAGAUGCAGUGUACCCG |
| RlmJ Me | UUGAACUCGCUGUGm6AAGAUGCAGUGUACCCG |
| DNAs | |
| KsgA MB | Alexa Fluor 488-CCGCCCCGCAGGTTCCCCTACGGCGG-DABCYL |
| RrmA MB | Alexa Fluor 488-CCGCCGTTTTTCAACATTAGTCGGCGG-DABCYL |
| RrmA MB-Cy3 | Cy3-CCGCCGTTTTTCAACATTAGTCGGCGG-BHQ2 |
| RsmE MB | Alexa Fluor 488-CGCGCCTTGTTACGACTTCGGCGCG-DABCYL |
| RlmJ MB | FAM-CGCGCATCTTCACAGCGCG-DABCYL |
| 16S MB | Alexa Fluor 647-CACTCCGCTGCCTCCCGTAGGAGTG-BHQ1 |
| 16S MB-G | Alexa Fluor 488-CACTCCGCTGCCTCCCGTAGGAGTG-DABCYL |
| 23S MB | Alexa Fluor 647-CGGCGAGCAAGTCGCTTCACCTACATATCGCCG-BHQ1 |
| KsgA BLK | CCGCC CCGCAGG TT CCCCTAC GG CGG |
| RrmA BLK | CCGCCG TTTTTCAA C ATTAGT CGG CGG |
| RsmE BLK | CGCG CC TTGTT A CGACTTC GGCGCG |
| HLP1 | AGTGGTAAGCGCCCTCCCGA |
| HLP2 | ACCCCAGTCATGAATCACAA |
| HLP3 | GCAGGTTCCCCTACGGTTA |
| HLP4 | TAAGGAGGTGATCCAACC |
RNA nucleotides complementary to MB sequences are shown in italics, with methylated bases or bases whose methylation is catalyzed by MTase shown in bold italics. DNA nucleotides complementary to rRNA sequences are shown in italics, with nucleotides complementary to bases methylated by the relevant methyltransferase in bold italics. The self-complementary sections of Molecular Beacons that fold into the stem are underlined. The structures of modified nucleosides, fluorophores and quenchers are given in Supplementary Fig. 1