Table 2.
Oligonucleotides
| Oligonucleotides | |||
|---|---|---|---|
| Purpose | Template | Name | Sequence |
| cRACE | |||
| met leader | - | FW144 | CACTCCAAGGCCATTTTCAA |
| - | FW145 | GTGATAATTGTTCAGTAAGCAT | |
| metI | - | FW156 | CCTGTCGATTGTCCTAGTTT |
| - | FW157 | CACGTACTAAAAATCCTACA | |
| 5′-RACE | |||
| 5′ RACE RNA adapter | CUAGUACUCCGGUAUUGCGGUACCCUUGUACGCCUGUUUUAUA | ||
| 5′ RACE RNA adapter primer | GTATTGCGGTACCCTTGT | ||
| metI | - | FW200 | CGTGGCTGAATGTAAGACTATA |
| - | Sa_lgsm02-Lext-Rev | TCAGCACCTTCTGCTAGTGGT | |
| metF | - | FW149 | GCGATGTTGAAGTGTGTACGTTT |
| - | FW161 | CGGTGTGATAATGTATAAACCATT | |
| ivt for in-line probing | |||
| T7 met leader | pJC1_tRNAi_deletion | FW088 | TTAACTAATACGACTCACTATAGGGTCTTATAACAGTTTAATGAAACGTAAAC |
| Sa.R_met-sRNA | GAAAAAATAAAAAAAGCTTCCGTCCTTCG | ||
| T7 short met leader | pJC1_tRNAi_deletion | FW130 | TTAACTAATACGACTCACTATAGGGATTCTTTACGCACGATTTTTTGTT |
| Sa.R_met-sRNA | GAAAAAATAAAAAAAGCTTCCGTCCTTCG | ||
| T7 short met leader Ter_destab | pBASE_Ter_destab | FW130 | TTAACTAATACGACTCACTATAGGGATTCTTTACGCACGATTTTTTGTT |
| FW159 | GAAAAAATAAAAAAAGAGTCGTTGAATCGTCA | ||
| T7 short met leader Ter_mutated_1 | 2.2 kb overlap PCR met leader Ter_mutated_1 fragment | FW130 | TTAACTAATACGACTCACTATAGGGATTCTTTACGCACGATTTTTTGTT |
| FW169 | GAAAAAATAAAAAAAGGATCGTTGCCTCGT | ||
| T7 short met leader Ter_mutated_2 | pBASE_Ter_mutated_2 | FW130 | TTAACTAATACGACTCACTATAGGGATTCTTTACGCACGATTTTTTGTT |
| FW211 | GAAAAAATAAAAAAAGCTTCCGTGCTTCGT | ||
| T7 short met leader Ter_mutated_3 | pBASE_Ter_mutated_3 | FW130 | TTAACTAATACGACTCACTATAGGGATTCTTTACGCACGATTTTTTGTT |
| FW212 | GAAAAAATAAAAAAAGCTTCCGTGCCTCGT | ||
| T7 short met leader Ter_mutated_4 | pBASE_Ter_mutated_4 | FW130 | TTAACTAATACGACTCACTATAGGGATTCTTTACGCACGATTTTTTGTT |
| FW213 | GAAAAAATAAAAAAAGCTTCCTGGCTTCGT | ||
| dsDNA probes | |||
| met leader | Newman | Sa_lgsm02_Fow | ATGTATTCTAAATGAGTCAGACAACC |
| Sa_lgsm02_Rev | CCGTCCTTCGTACCCGAATGA | ||
| metI | Newman | Sa_lgsm02-Lext_Fow | ACATCAAGTGGAATGTCAGCCA |
| Sa_0431_R | CTATTGGTGAAAGTGTTGCGCCA | ||
| metI 5′ | Newman | FW137 | |
| Sa_0431-R_RT | CGAATGATGCAATACCATGCTCA | ||
| metC | Newman | Sa_0430_F | GCTCGAACAAATCGAGGGTGCCA |
| Sa_0430_R | ACGAAAGCCAATAACGGCAC | ||
| metC 3′ | Newman | FW140 | GCCTCCTTTAATGCGTATTTGAT |
| FW141 | GCTGATGAGTCTAAAGCACAA | ||
| metF | Newman | Sa_0429_F | ACAACTCGTTCAATGTGGTGC |
| Sa_0429_R | TCTGCGAGTGTTACCGCATCTAC | ||
| metF 3′ | Newman | FW138 | CTCCTTGTGAGCAGTAATAGATT |
| FW139 | GGTATTAACACTGACGGTGAT | ||
| metE | Newman | Sa_metE_F | TGATGGTCGTAATGTATGGGCA |
| Sa_metE_R | CGTTTGTTCTTCCAATCTGCACG | ||
| mdh | Newman | FW051 | GCAACTTGGGTTGATTTAACGCAT |
| FW052 | GCCACGAGTTGGTAATTGATCTA | ||
| ssDNA probes | |||
| 16S rRNA | - | 16S_rDNA_R | TACGGCTACCTTGTTACGACTT |
| 5S rRNA | - | 5SrRNA | CAGTCCGACTACCATCGGCG |