TABLE 2.
Oligonucleotides
| Oligonucleotidea | Sequence (5′-3′) | Position (start, end)b |
|---|---|---|
| RlxNco (−) | AGC CAT GGCAGTTACAAAGATACATCCc | −21857, −21835 |
| RlxXho (+) | TACTCGAGTAGCTCTTGCGTCCATTCCTTTCCC | 20532, 20556 |
| RlxNXho (+) | TACTCGAGCGCTCTGGTGATAACGCGGCC | 21116, 21137 |
| RlxpBADXho (+) | TACTCGAGTTCATAGCTCTTGCGTCCATTCCTTTCCC | 20529, 20556 |
| C1 (+) | AAGGCAGGGACGGGGCAGGCCGTTc | 22212, 22233 |
| C2 (−) | GCCGCGTCCGTTTTGCTTGTTGG | −22209, −22187 |
| FmutNic (+) | TAAGCATAGGGAGTGTAGCC | 22263, 22245 |
| RmutNic (−) | CTACGTTACTGTTTCTCCAC | −22265, −22284 |
| MutAF (+) | CACTCC CGGAAAAACGGCCTG | 22245, 22225 |
| MutA1R (−) | GCTACAGTACCTATGCTTGCTACGTTACTG | −22246, −22275 |
| MutA2R (−) | CATACACTCCCTATGCTTGCTACGTTACTG | −22248, −22275 |
| MutBF (+) | ATCGCGAAACCCCTGAATGGAAAGG | 22158, 22176 |
| MutBR (−) | TTCCCCAACAAGCAAAACGGAC | −22204, −22183 |
| MobCNdeI (−) | GACATATGGCAAACAGAAAGC G | −22147, −22131 |
| MobCFHindIII (−) | ATAAGCTTGGAAAGGACGGTGAAGCA | −22165, −22147 |
| MobCREcoRI (+) | ATGAATTCTCGATGTAGTCAA GGG C | 21793, 21812 |
| 30R (−) | ATAAGCTTACTTTTAGCGGGAGCTGC | −22389, −22370 |
| 29F (+) | ATGAATTCACCGTCCTTTCCATTCAG | 22150, 22170 |
| O30DF (−) | CTAAGCTTGAAACAGTAACGTAGCAAGC | −22279, −22260 |
| 27FEcoRI (+) | ATGAATTCATGC CGGAAAAGCCTTGAA | 20129, 20148 |
| 28RHindIII (−) | ATAAGCTTATGAGTATTCCACGAATGA | −20533, −20514 |
| 184OriF/EcoRI (+) | CTGAATTCAGCAAGCATAGGGAGTGTAGCCACTCCCTGCAGAAGCTTTGACACAGTGCCG | 22266, 22239 |
| 184R/EcoRI (−) | TAGAATTCCGGATGAGCATTCATCAGG | |
| HTH-EcoRI (−) | TGAATTCTGGCATCCTCTGTTTTACT | −22404, −22385 |
| RlxXbaI (+) | AATCTAGATACTCATAGCTCTTGCGTCC | 20525, 20545 |
| YXbaI (+) | ATCTAGACTATCTCTGTTCCAGCGGGAAG | 19742, 19763 |
| Ori34F (+)d | TAACGTAGCAAGCATAGGGAGTGTAGCCACTCCC | 22272, 22239 |
| Ori34R (−)d | GGGAGTGGCTACACTCCCTATGCTTGCTACGTTA | −22239, −22272 |
| 28RpACY (−) | ACTCCACCGCTGATGACATCAG | |
| 28FpACY (+) | CTTTATTCACATTCTTGCCCG | |
| 27f (+)e | GCTCTAAGTGCGTAGGTTTC | 20166, 20185 |
| 28f2 (+)e | AAACTTTCCCGGCTTGATCT | 21231, 21250 |
| 28f1 (+)e | CCGCAGGAAATCATCAAAAT | 21273, 21292 |
| 28r1 (−)e | GTGCAAGGAAAACGGATTGT | −21435, −21416 |
| 29f2 (+)e | CAGGGACGCGCAGCACGATT | 22108, 22127 |
| 29r2 (−)e | GAGATACAGAAGATCGGCGT | −21967, −21948 |
| 30f (+)e | CGATGATCGGCAGGTATTCT | 22470, 22489 |
| 30r (−)e | ATTGACTGGCGCTATCTTGC | −22668, −22649 |
| Race 1(+)e | GATGATCGGCAGGTATTCTT | 22471, 22490 |
| Race 2(+)e | ATAAGCTGTATGACAACCGG | 22595, 22614 |
a
+, sense primer; −, antisense primer.
b
Nucleotide numbering according to GenBank accession number AF192329.1.
c
Restriction sites used in cloning are underlined. 5′-end phosphorylated nucleotides are in bold.
d
Oligonucleotides used in nicking assay.
e
Oligonucleotides used in RT-PCR and 5′ RACE assays.