TABLE 2.
Oligonucleotide primers used in this work
| Primer | Sequencea | Positionb | Application |
|---|---|---|---|
| JC5 | 5′-CATATGAAACCAGGACGGAGACCCACAGAAGGG-3′ | +1 | Upper primer for cloning coding region of Magnetococcus lexA gene and amplifying lexA fragment in RT-PCR experiments |
| JC6 | 5′-GGATCCGTCGACTTATTCATTATTGTTGGCGGCCCCGTGG-3′ | +672 | Lower primer for cloning coding region of Magnetococcus lexA gene and amplifying lexA fragment in RT-PCR experiments |
| JC7 | 5′-GAGGTGGAAGGCCATTCCTGTTGCC-3′ | −261 | Upper primer to amplify LexA1 probe |
| JC8DIG | 5′-DIG-CCAGTTTCTGCACCTGTTCATGGGC-3′ | +468 | Lower primer to amplify DIG-labeled probe fragments of lexA promoter |
| JC8 | 5′-CCAGTTTCTGCACCTGTTCATGGGC-3′ | +468 | Lower primer to amplify unlabeled probe fragments of lexA promoter |
| JC13 | 5′-CAGATCCATATTGGTTACTTACCG-3′ | −178 | Upper primer to amplify LexA2 probe |
| JC14 | 5′-AACTTACACCTTATTAAAATAAGG-3′ | −100 | Upper primer to amplify LexA3 probe |
| JC15 | 5′-TAAAATAAGGTCACAAGAGAGC-3′ | −86 | Upper primer to amplify LexA4 probe |
| JC16 | 5′-AACTTACGGGGTATTAAAATAAGG-3′ | −100 | JC14 with ACCT-to-GGGG change in LexA3 probe |
| JC22 | 5′-AACTTACACCTTATTAAAAATAAGGTCAC-3′ | −100 | JC14 with addition of an A at position −84 in LexA3 probe |
| JC23 | 5′-AACTTACACCTTATTAAAAAATAAGGTCAC-3′ | −100 | JC14 with addition of two A's at position −84 in LexA3 probe |
| JC24 | 5′-AACTTACACCTTATTAAAAAAATAAGGTCAC-3′ | −100 | JC14 with addition of three A's at position −84 in LexA3 probe |
| JC26 | 5′-AACTTACGCCTTATTAAAATAAGG-3′ | −100 | JC14 with A-to-G change at position −93 in LexA3 probe |
| JC27 | 5′-AACTTACAGCTTATTAAAATAAGG-3′ | −100 | JC14 with C-to-G change at position −92 in LexA3 probe |
| JC28 | 5′-AACTTACACGTTATTAAAATAAGG-3′ | −100 | JC14 with C-to-A change at position −91 in LexA3 probe |
| JC29 | 5′-AACTTACACCGTATTAAAATAAGG-3′ | −100 | JC14 with T-to-A change at position −90 in LexA3 probe |
| JC30 | 5′-AACTTACACCTGATTAAAATAAGG-3′ | −100 | JC14 with T-to-G change at position −89 in LexA3 probe |
| JC31 | 5′-AACTTACACCTTGTTAAAATAAGG-3′ | −100 | JC14 with A-to-G change at position −88 in LexA3 probe |
| JC32 | 5′-AACTTACACCTTAGTAAAATAAGG-3′ | −100 | JC14 with T-to-G change at position −87 in LexA3 probe |
| JC33 | 5′-AACTTACACCTTATGAAAATAAGG-3′ | −100 | JC14 with T-to-G change at position −86 in LexA3 probe |
| JC34 | 5′-AACTTACACCTTATTGAAATAAGGTCAC-3′ | −100 | JC14 with A-to-G change at position −85 in LexA3 probe |
| JC35 | 5′-AACTTACACCTTATTAGAATAAGGTCAC-3′ | −100 | JC14 with A-to-G change at position −84 in LexA3 probe |
| JC36 | 5′-AACTTACACCTTATTAAGATAAGGTCAC-3′ | −100 | JC14 with A-to-G change at position −83 in LexA3 probe |
| JC37 | 5′-AACTTACACCTTATTAAAGTAAGGTCAC-3′ | −100 | JC14 with A-to-G change at position −82 in LexA3 probe |
| JC38 | 5′-AACTTACACCTTATTAAAAGAAGGTCAC-3′ | −100 | JC14 with T-to-G change at position −81 in LexA3 probe |
| JC39 | 5′-AACTTACACCTTATTAAAATGAGGTCACAAGAGAG-3′ | −100 | JC14 with A-to-G change at position −80 in LexA3 probe |
| JC40 | 5′-AACTTACACCTTATTAAAATAGGGTCACAAGAGAG-3′ | −100 | JC14 with A-to-G change at position −79 in LexA3 probe |
| JC41 | 5′-AACTTACACCTTATTAAAATAACGTCACAAGAGAG-3′ | −100 | JC14 with G-to-C change at position −78 in LexA3 probe |
| JC42 | 5′-AACTTACACCTTATTAAAATAAGCTCACAAGAGAG-3′ | −100 | JC14 with G-to-C change at position −77 in LexA3 probe |
| JC43 | 5′-AACTTACACCTTATTAAAATAAGGGCACAAGAGAG-3′ | −100 | JC14 with T-to-G change at position −76 in LexA3 probe |
| JC11 | 5′-GGTTTTCCGTGAAAAAGTCTCATAACCGCG-3′ | −308 | Upper primer to amplify umuDC promoter region |
| JC12 | 5′-AGCCGGTACCGCCGGATGCACCTGC-3′ | +228 | Lower primer to amplify umuDC promoter region |
| JC46 | 5′-ACATCCCCATCAATCCGCACCATGG-3′ | −342 | Upper primer to amplify recA promoter region |
| JC47 | 5′-CAGTGCTTTGCTCTTATCTTTATCC-3′ | +32 | Lower primer to amplify recA promoter region |
| JC48 | 5′-CCAATGGGGCTCTAACTGCGTGGGG-3′ | −271 | Upper primer to amplify uvrA promoter region |
| JC49 | 5′-CAGGTTGTGTTCCCGGGCACCACGG-3′ | +48 | Lower primer to amplify uvrA promoter region |
| JC50 | 5′-AACCGCCCCATTGCGGTGCCCGGCG-3′ | −270 | Upper primer to amplify recN promoter region |
| JC51 | 5′-CGACATGCTTCAATGGTGAGTTGACG-3′ | +30 | Lower primer to amplify recN promoter region |
| JC19 | 5′-ACCGCGATACCTAATATTTATTAGG-3′ | −55 | Upper primer to amplify umuD probe |
| JC12DIG | 5′-AGCCGGTACCGCCGGATGCACCTGC-3′ | +228 | Lower primer to amplify DIG-labeled umuD probe |
| JC57 | 5′-ACCGCGATGCCTAATATTTATTAGG-3′ | −55 | JC19 with A-to-G change at position −48 in umuD probe |
| JC58 | 5′-ACCGCGATAGCTAATATTTATTAGG-3′ | −55 | JC19 with C-to-G change at position −47 in umuD probe |
| JC59 | 5′-ACCGCGATACGTAATATTTATTAGG-3′ | −55 | JC19 with C-to-G change at position −46 in umuD probe |
| JC60 | 5′-ACCGCGATACCGAATATTTATTAGG-3′ | −55 | JC19 with T-to-G change at position −45 in umuD probe |
| JC61 | 5′-ACCGCGATACCTGATATTTATTAGG-3′ | −55 | JC19 with A-to-G change at position −44 in umuD probe |
| JC62 | 5′-ACCGCGATACCTAGTATTTATTAGG-3′ | −55 | JC19 with A-to-G change at position −43 in umuD probe |
| JC63 | 5′-ACCGCGATACCTAAGATTTATTAGG-3′ | −55 | JC19 with T-to-G change at position −42 in umuD probe |
| JC64 | 5′-ACCGCGATACCTAATGTTTATTAGGTATCGCTGC-3′ | −55 | JC19 with A-to-G change at position −41 in umuD probe |
| JC65 | 5′-ACCGCGATACCTAATAGTTATTAGGTATCGCTGC-3′ | −55 | JC19 with T-to-G change at position −40 in umuD probe |
| JC66 | 5′-ACCGCGATACCTAATATGTATTAGGTATCGCTGC-3′ | −55 | JC19 with T-to-G change at position −39 in umuD probe |
| JC67 | 5′-ACCGCGATACCTAATATTGATTAGGTATCGCTGC-3′ | −55 | JC19 with T-to-G change at position −38 in umuD probe |
| JC68 | 5′-ACCGCGATACCTAATATTTGTTAGGTATCGCTGC-3′ | −55 | JC19 with A-to-G change at position −37 in umuD probe |
| JC69 | 5′-ACCGCGATACCTAATATTTAGTAGGTATCGCTGC-3′ | −55 | JC19 with T-to-G change at position −36 in umuD probe |
| JC70 | 5′-ACCGCGATACCTAATATTTATGAGGTATCGCTGC-3′ | −55 | JC19 with T-to-G change at position −35 in umuD probe |
| JC71 | 5′-ACCGCGATACCTAATATTTATTGGGTATCGCTGC-3′ | −55 | JC19 with A-to-G change at position −34 in umuD probe |
| JC72 | 5′-ACCGCGATACCTAATATTTATTACGTATCGCTGC-3′ | −55 | JC19 with G-to-C change at position −33 in umuD probe |
| JC73 | 5′-ACCGCGATACCTAATATTTATTAGCTATCGCTGCTC-3′ | −55 | JC19 with G-to-C change at position −32 in umuD probe |
| JC74 | 5′-ACCGCGATACCTAATATTTATTAGGGATCGCTGCTC-3′ | −55 | JC19 with T-to-G change at position −31 in umuD probe |
| 637rv | 5′-CCATCCATGTCACTACAGGTC-3′ | +1542 | Lower primer to amplify lexA-ORF637 fragment in RT-PCR experiments |
| 637fwd | 5′-CTTGGATTGGGTGAAGCTTTGCC-3′ | +1542 | Upper primer to amplify ORF637-rumA and ORF637-ORF640 fragments in RT-PCR experiments |
| 639rv | 5′-ATCGGCTCCAATGATCGATCC-3′ | +3120 | Lower primer to amplify ORF637-rumA fragment in RT-PCR experiments |
| 640rv | 5′-ATGAAGGTATTCAACCCGGCCC-3′ | +3787 | Lower primer to amplify ORF637-ORF640 fragment in RT-PCR experiments |
a
Added restriction sites are italicized; nucleotide changes are underlined.
b
Position of the 5′ end of the oligonucleotide with respect to the proposed translational starting point of each Magnetococcus MC-1 gene.