Table 1.
Sequence of primers for PCR, molecular beacon probes and their specific targets
| PCR Primers, Probes and Targets | Sequence | Length | Fluorophore/Quencher | Tm Probe-target/Stem |
|---|---|---|---|---|
| RecF | 5' GTG GAT CTA TTG TAT TAG ATG AGG CTC TCG 3' | 30 | - | - |
| RecR | 5' GCC AAA GTT CTG CAA CAT TAA CAC CTA AAG 3' | 30 | - | - |
| NidoF | 5' CCA GCC ACA GAA TAC CAT CC 3' | 20 | - | - |
| NidoR | 5' GGA CAT ACT CTG CTG CCA TC 3' | 20 | - | - |
| Nidogen | 5' CGG CGCACC CAG CTT CGG CTC AGT AGC GCC G 3' | 31 | TET/BHQ1 | 77°C/84°C |
| Nidogen Target | 5' ta GGC GCT ACT GAG CCG AAG CTG GGT G at 3' | 29 | - | - |
| RecA1 | 5' CCC GCGCGT CTG GCA AGA CTA CTT TAA CTC TTC GCG GG 3' | 38 | FAM/BHQ1 | 68°C/71°C |
| RecA1 Target | 5' ta GAA GAG TTA AAG TAG TCT TGC CAG ACG at 3' | 31 | - | - |
| RecA2 | 5' CGCGAGTCG TCT GGC AAG ACT ACT TTA ACTCGCG 3' | 34 | FAM/DABCYL | 73°C/67°C |
| RecA2 Target | 5' ttG AGT TAA AGT AGT CTT GCC AGA CGA CTC tt 3' | 32 | - | - |
| RecA3 | 5' CTG GCGGAT ATC CTA GGG GGCGC CAG 3' | 26 | FAM/BHQ1 | 75°C/75°C |
| RecA3 Target | 5' ttG CGC CCC CTA GGA TAT CCG CCt t 3' | 25 | - | - |
Underlined letters in molecular beacons sequence indicate stem sequence and bold letters indicate the probe (loop) sequence. There is an overlaps between probe and stem sequence in RecA3 molecular beacon.
Nucleotides denoted by small case letters in the targets indicate non-template based tails
FAM-Fluorescein, TET-Tetrachlorofluorescein, DABCYL-[4 - ((4 - (dimethylamino)phenyl)azo) benzoic acid] and BHQ-1 = Black Hole Quencher 1