Table 3 List of primers used for PCR amplification of protein-encoding genes from Treponema denticola strains
From: Multilocus sequence analysis of Treponema denticolastrains of diverse origin
| Gene | Primer | Sequence(5′to 3′) | Strains amplified |
|---|---|---|---|
| dnaN | dnaNF | ATGAAAATAAGTTTTGACAGAGACAC | dnaF + dnaR: all strains (55-50°C) |
| dnaNR | TTACTCCGTCTGCATAGGC | ||
| recA | recAF1 | GTGGCAAAAGCAAAAAAC | recAF1 + recAR1: most strains (55-47°C) |
| recAR1 | TTAAAAAAGACTGTCGTCCG | recAF2 + recAR2: ATCC 700768, MS25 (54-47°C) | |
| recAF2 | TTCATATTGGCCGCATTTG | recAF1 + recArecAR2: ATCC 700771 (55-49°C) | |
| recAR2 | TTGTGTACTCATAATGCCGCTC | ||
| recAF | GTGGCAAAAGCAAAAAACGAAG | recAF + recAR: OMZ852, OMZ853, NY531, NY553 (58-53°C) | |
| recAR | TTAAAAAAGACTGTCGTCCGCC | ||
| radC | radCF1 | ATGATAGACTATAAAAATTCGTCCAATAC | radCF1 + radCR1: most strains (55-50°C) |
| radCR1 | TTAAATATCAAACCTCGTTCCG | radCF1 + radCR2: MS25 (55-49°C) | |
| radCF2 | AACATGGCTTTCCGAAATC | radCF2 + radCR1: ATCC 700768 (55-49°C) | |
| radCR2 | GTGCAGCGGCTCTAAAAG | ||
| ppnK | TDE1591F1 | ATATGGATCCCATATGAAAAAAG | TDE1591F1 + TDE1591R1: most strains (52-45°C) |
| TDE1591R1 | AATTCTCGAGTCAATTCAGTTTGGG | TDE1591F2 + TDE1591R2: OKA3, MS25,GM1, ST10A, | |
| TDE1591F2 | AGCTACCCTGCCCTAATTTC | ATCC 700768, ATCC 700771 (57-52°C) | |
| TDE1591R2 | AACATCCTTAAAAAGCGGC | ||
| flaA | TDE1712F | ATGAAAAAAACATTTATACTTGTTG | TDE1712F + TDE1712R: all strains (52-46°C) |
| TDE1712R | TTATTGTTGGTTCTTTTCGG | ||
| era | eraF1 | ATGAACAGCGGAGTTGTAAC | eraF1 + eraR1: most strains (55-50°C) |
| eraR1 | TTAATACGAGATTTTTTTTATGATATTATC | ||
| eraF2 | GGTACTTGTGCTTACCGAAAAC | eraF2 + eraR2: MS25 (54-47°C) | |
| eraR2 | CCGACACAATCGAGGAAG | ||
| eraF4 | CGCTTAGAAGAAGGGGATGC | eraF4, eraR4 separately used for direct chromosome sequencing of ATCC 700768† | |
| eraR4 | CTTTTTCGACATAGAGGAAGGC | ||
| pyrH | pyrHF | ATGGTAACTGTTTTGTCGGT | pyrHF + pyrHR: all strains (54-47°C) |
| pyrHR | TTAGCCGATTACCGTTCCTT |