TABLE 1.
Primers, cycling conditions, and fragment sizes for the N3M-PCR assay
| Primer | Sequence | Cycling conditions | No. of cycles and final step (if any) | Fragment size (bp) |
|---|---|---|---|---|
| Gp40F-1 | 5′TCTTAGGAGCAGCAGGAAGCACTATGGG | 94°C for 5 min, 50°C for 1 min, 72°C for 2 min | 1 | 583 |
| Gp41R-1 | 3′AACGACAAAGGTGAGTATCCCTGCCTAA | 94°C for 30 s, 50°C for 30 s, 70°C for 1 min | 30; 10 min at 72°C | |
| Gp46F-2 | 5′ACAATTATTGTCTGGTATAGTGCAACAGCA | 94°C for 2 min, 50°C for 50 s, 72°C for 1 min | 1 | 460 |
| Gp47R-2 | 3′TTAAACCTATCAAGCCTCCTACTATCATTA | 94°C for 30 s, 50°C for 30 s, 70°C for 1 min | 35; 10 min at 72°C | |
| Gag f-2 | 5′ATGGGTGCGAGAGCGTCARTATTA A | 94°C for 5 min, 52°C for 1 min, 72°C for 2 min | 1 | 1,242 |
| Gag e-2 | 3′TCCAACAGCCCTTTTTCCTAGG | 94°C for 30 s, 52°C for 30 s, 70°C for 1 min | 30; 10 min at 72°C | |
| 306 | 5′GGGAAA AAATTCGGTTAAGGCC | 94°C for 2 min, 50°C for 50 s, 72°C for 1 min | 1 | 671 |
| Cn-gag | 3′TAGTTCCTGCTATRTCACTTCC | 94°C for 30 s, 52°C for 30 s, 70°C for 1 min | 35; 10 min at 72°C | |
| Pol-1 | 5′CCCTACAATCCCCAA AGTCAAGG | 94°C for 30 s, 50°C for 15 s, 72°C for 45 s | 35; 10 min at 72°C | 323 |
| Pol-2 | 3′TACTGCCCCTTCACCTTTCCA | |||
| Pol-3 | 5′TAAGACAGCAGTACAAATGGCAG | 94°C for 30 s, 50°C for 15 s, 72°C for 30 s | 30; 10 min at 72°C | 175 |
| Pol-4 | 3′GCTGTCCCTGTAATA AACCCG | |||
| β-actin-1 | 5′ACACAACTGTGTTCACTAGC | 94°C for 30 s, 50°C for 15 s, 72°C for 45 s | 35; 10 min at 72°C | 300 |
| β-actin-2 | 3′TGGTCTCCTTAAACCTGTCTTG |