Table 2. Single strand primers and probes used for PCR and RPA reactions.
| Target genes | Primer name | Sequence (5′–3′) and modification | Product length | Primer location | Genbank accession no. | Reference |
|---|---|---|---|---|---|---|
| ddl |
ddl-F (RPA)a ddl-R (RPA)a |
ACCCAAGTGGACAGACAGAGGAAGGCTTTA TTCCATCTTCCCCGTTTGGCCCATGTAAAACT | 156 bp | 242–271 368–397 |
AY489046.1 | This study |
|
ddl-R (RPA-LF) ddl-P (RPA-LF) |
Biotin-CATAAGGCATATTCAATGTCTCTAAGAAGC FAM-CGGGAGAAATCAAAGAAGAAGGAGCCATCG-[THF]-TTTTCCAGTTTTACA-C3-Spacer |
This study | ||||
| vanA |
vanA-F (PCR) vanA-R (PCR) |
GGGAAAACGACAATTGC GTACAATGCGGCCGTTA |
941 bp | 176–192 891–907 |
NC_014475.1 | Dutka-Malen, Evers & Courvalin (1995) |
|
vanA-F (RPA) vanA-R (RPA) |
TTGCGCGGAATGGGAAAACGACAATTGCTATT CAAAAGGGATACCGGACAATTCAAACAGACC |
194 bp | 165–196 328–358 |
NC_014475.1 | This study | |
|
vanA-R (RPA-LF) vanA-P (RPA-LF) |
Biotin-CAAAAGGGATACCGGACAATTCAAACAGACC FAM-GATGTAGCATTTTCAGCTTTGCATGGCAAG-[THF]-CAGGTGAAGATGGAT-C3-Spacer |
This study | ||||
| vanB |
vanB-F (PCR) vanB-R (PCR) |
ATGGGAAGCCGATAGTC GATTTCGTTCCTCGACC |
635 bp | 174–190 792–808 |
NC_004668.1 | Dutka-Malen, Evers & Courvalin (1995) |
|
vanB-F (RPA) vanB-R (RPA) |
GAGGATGATTTGATTGTCGGCGAAGTGGAT TTTGCCGTTTCTTGCACCCGATTTCGTTCCTC |
165 bp | 664–693 765–795 |
NC_004668.1 | This study | |
|
vanB-R (RPA-LF) vanB-P (RPA-LF) |
Biotin- TTTGCCGTTTCTTGCACCCGATTTCGTTCCTC FAM-CAAATCCGGCTGAGCCACGGTATCTTCCGC-[THF]-TCCATCAGGAAAACG-C3-Spacer |
This study |
Notes.
a
The ddl RPA primer pair was used in both PCR and RPA reaction.
- F
- forward primer
- R
- reverse primer
- FAM
- 6-Carboxyfluorescein
- THF
- tetrahydrofuran residue, an internal abasic nucleotide
- C3-Spacers
- a polymerase extension blocking group