Table 1.
List of oligonucleotides used for this study
| Primers | Sequence | Orientation | Amplicon size (bp) |
Annealing temperature (°C) |
|---|---|---|---|---|
| PROMOTER ANALYSIS | ||||
| Gene 14-upstream sequence primers | ||||
| For cloning into pPROBE-NT | ||||
| RRG 183* | 5' GACTCTAGAttgctcaacccataaaataatg | Forward | 596 | 50 |
| RRG 184 | 5' AGTGAGCTCtttataaaagataataaaaatttaag | Reverse | ||
| For cloning into pBlue-TOPO | ||||
| RRG 217 | 5' attgctcaaccataaaataatggga | Forward | 581 | 48 |
| RRG 218 | 5' gttaataaaccttttataaaag | Reverse | ||
| RRG 267 | 5' cagttaactttctgtaaacttc | Forward | 521 | 48 |
| RRG 218** | Reverse | |||
| RRG 268 | 5' atcataagtttacaataatgtc | Forward | 461 | 48 |
| RRG 218 | Reverse | |||
| RRG 269 | 5' cgttttctgctttattagaatg | Forward | 400 | 48 |
| RRG 218 | Reverse | |||
| RRG 270 | 5' gttccgtatttattaatatatg | Forward | 350 | 48 |
| RRG 218 | Reverse | |||
| RRG 271 | 5' catgtactgaatttgtgatttg | Forward | 286 | 48 |
| RRG 218 | Reverse | |||
| RRG 272 | 5' ggataagtactttagcaagtgg | Forward | 222 | 48 |
| RRG 218 | Reverse | |||
| RRG 273 | 5' taagtagtaaagttaactatag | Forward | 169 | 48 |
| RRG 218 | Reverse | |||
| RRG 274 | 5' acttttgttgtaaatttgaaag | Forward | 105 | 48 |
| RRG 218 | Reverse | |||
| RRG 217 | Forward | 516 | 50 | |
| IG14-35 del R | 5' (PO4)-gtctagaatataaaatttctttc | Reverse | ||
| IG14-10 del F | 5' (PO4)-taaatttttattatcttttataaaaggtttattaac | Forward | 8366 | 56 |
| IG14-10 del R | 5' (PO4)-atgaaagaaataaagaaaagcaagtctag | Reverse | ||
| IG14-35 del F | 5' (PO4)-ttctttatttctttcattattc | Forward | 8366 | 48 |
| IG14-35 del R | Reverse | |||
| IG14-10 del F | Forward | 8343 | 51 | |
| IG14-35 del R | Reverse | |||
| Gene 19-upstream sequence primers | ||||
| For cloning into pPROBE-NT | ||||
| RRG 185 | 5' GACTCTAGActtttaattttattattgccacatg | Forward | 334 | 61 |
| RRG 186 | 5' AGTGAGCTCaatagtgacaaataaattaacaatag | Reverse | ||
| For cloning into pBlue-TOPO | ||||
| RRG 185 | Forward | 308 | 60 | |
| RRG 445 | 5' atataacctaatagtgacaaataaattaac | Reverse | ||
| RRG 275 | 5' gtggcaaaagaatgtagcaataag | Forward | 239 | 50 |
| RRG 445 | Reverse | |||
| RRG 276 | 5' gtgctgtttttctcacctttacac | Forward | 188 | 63 |
| RRG 445 | Reverse | |||
| RRG 277 | 5' ctgacgtaatatattaaattttcc | Forward | 125 | 55 |
| RRG 445 | Reverse | |||
| RRG 185 | Forward | 267 | 50 | |
| IG19-35 del R | 5' (PO4)-gtcagaatataaatttttgtataaaatatcg | Reverse | ||
| IG19-10 del F | 5' (PO4)-taatttatttgtcactattaggttat | Forward | 8112 | 56 |
| IG19-10 del R | 5' (PO4)-gtagaagtgtcatataaaagcaag | Reverse | ||
| IG19-35 del F | 5' (PO4)-ttatatgacacttctactattgttaatttatttg | Forward | 8112 | 61.5 |
| IG19-35 del R | Reverse | |||
| IG19-10 del F | Forward | 8088 | 58 | |
| IG19-35 del R | Reverse | |||
| PRIMER EXTENSION ANALYSIS | ||||
| Gene 14 | ||||
| RRG 14-5'rev | 5' gccttctctgctgtcgttgattcc | NA | 52 | |
| Gene 19 | ||||
| RRG 20-PEXT | 5' cgttaataccactacctgctgggtcg | NA | 58 | |
| RRG 44 | 5' cgcttccgtcccaattttgcttc | NA | 58 | |
| IN VITRO TRANSCRIPTION ASSAY | ||||
| Gene 14 upstream full-length+lac Z segment | ||||
| RRG 217 | 5' attgctcaaccataaaataatggga | Forward | 882 | 50 |
| RRG 226 | 5' cgccattcgccattag | Reverse | ||
| RRG 218 | 5' gttaataaaccttttataaaag | Forward | 882 | 50 |
| RRG 226 | Reverse | |||
| Gene 19 upstream full-length+lac Z segment | ||||
| RRG 217 | 5' attgctcaaccataaaataatggga | Forward | 601 | 50 |
| RRG 226 | Reverse | |||
| RRG 445 | 5' atataacctaatagtgacaaataaattaac | Forward | 601 | 50 |
| RRG 226 | Reverse | |||
| IN VITRO TRANSCRIPTION COUPLED TRANSLATION ASSAY | ||||
| RRG 185 | 5' gactctagacttttaattttattattgccacatg | Forward | 848 | 58 |
| RRG 247 | 5' tccggctcgtatgttgtgtg | Reverse | ||
* Text in capital letters refers to sequences inserted for creating restriction enzyme sites. ** Primer sequences were presented only once when a primer was described for the first time.