TABLE 4.
PCR primers for isolation of patient-specific RT-PCR primer binding sites
| Sequence target(s) | Primer (reference) | Geneb | Strandc | Positiond
|
Sequencee | |
|---|---|---|---|---|---|---|
| 5′ | 3′ | |||||
| usRNA, vRNAex | Mf219 | gag | + | 1273 | 1304 | AAGGCTTTCAGCCCAGAAGTAATACCCATGTT |
| Mf06 | gag | + | 1296 | 1325 | ACCCATGTTTTCAGCATTATCAGAAGGAGC | |
| Mf118 | gag | + | 1309 | 1332 | GCATTATCAGAAGGAGCCACCCCA | |
| Mf119 | gag | + | 1326 | 1354 | CACCCCACAAGATTTAAACACCATGCTAA | |
| Mf117 (46) | gag | − | 1571 | 1544 | ATTTCTCCTACTGGGATAGGTGGATTAT | |
| Mf218 | gag | − | 1623 | 1597 | GCTATACATTCTTACTATTTTATTTAA | |
| Sk39 (46) | gag | − | 1658 | 1631 | TTTGGTCCTTGTCTTATGTCCAGAATGC | |
| Spliced msRNA | CR5 (70) | U5/PBS | + | 626 | 648 | TCTCTAGCAGTGGCGCCCGAACA |
| Mf104 | psi/env | + | 721 | 5780 | CAAGAGGCGAGGGGAGGCGACTGAAT | |
| Mf103 | vpr/tat | + | 5833 | 5862 | GGAGCCAGTAGATCCTAGACTAGAGCCCTG | |
| Pr1 (71) | tat | + | 5853 | 5877 | TAGAGCCCTGGAAGCATCCAGGAAG | |
| Mf221 | tat | + | 5889 | 5914 | CTGCTTGTAACAAGTGTTATTGTAAA | |
| Mf236 | tat | + | 5907 | 5931 | ATTGTAAAAAGTGTTGCTTTCATTG | |
| msRNA exon4/5a | Mf238 | vpu | − | 6117 | 6087 | GCTATTATTGCTGCTACTACTAATGCTACTA |
| Mf239 | vpu | − | 6152 | 6120 | TATATTCTATGAATACTATGGACCACACAACTA | |
| Mf240 | vpu | − | 6201 | 6167 | CTTATTCTATCAATTAACCTGTCTATTTTTCTTTG | |
| Mf237 | vpu | − | 6251 | 6225 | ATTCTTCCTGATCCCCTTCACTCTCAT | |
| msRNA exon7a | M159 (50) | gp41 | + | 8079 | 8106 | CTGGATGAGATTTGGGATAACATGACCT |
| Mf161 | gp41 | + | 8121 | 8152 | AGAGAAATTGACAATTACACAAGCTTAATATA | |
| Mf160 | gp41 | + | 8148 | 8172 | ATATACACCTTAATTGAAGAATCGC | |
| Mf214 | gp41 | + | 8317 | 8349 | TTTTTGCTGTACTTTCTATAGTGAATAGAGTTA | |
| Mf222 | gp41 | + | 8350 | 8379 | GGCAGGGATATTCACCATTATCGTTTCAGA | |
| Mf224 | gp41 | + | 8361 | 8388 | TCACCATTATCGTTTCAGACCCACCTCC | |
| Spliced msRNA | Mf223 | gp41 | − | 8517 | 8493 | GGCACAGGCTCCGCAGATCGTCCCA |
| Mf220 | gp41 | − | 8533 | 8510 | CGGTGGTAGCTGAAGAGGCACAGG | |
| Mf215 | gp41 | − | 8552 | 8526 | CAAGAGTAAGTCTCTCAAGCGGTGGTA | |
| Mf156 (50) | gp41 | − | 8567 | 8542 | AATCCTCGTTACAATCAAGAGTAAGT | |
| Mf116 | gp41 | − | 8619 | 8589 | GATTCCACCAATATTTGAGGGCTTCCCACCC | |
| Mf121 | gp41 | − | 8681 | 8652 | GGCTGTGGCATTGAGCAAGCTAACAGCACT | |
| Mf105 | gp41 | − | 8706 | 8682 | TATCTGTCCCCTCAGCTACTGCTAT | |
| mascM (24) | nef | − | 9096 | 9068 | TAGCCCTTCCAGTCCCCCCTTTTCTTTTA | |
a
Exon numbering of spliced RNA is according to the work of Schwartz et al. (58).
b
Genes and landmarks of the HIV-1 genome are given as compiled in the Los Alamos HIV database (www.hiv.lanl.gov).
c
+, coding strand of the proviral genome; −, noncoding strand.
d
Numbering on the Hxb2 genome according to the software provided by the Los Alamos HIV database (SEQUENCE LOCATOR; www.hiv.lanl.gov).
e
Sequences are given 5′ to 3′ from left to right.