TABLE 5.
PCR primers used for patient-specific real-time PCR
| PCR target | Primer (reference)a | Functionb | Strandc | Positiond
|
Sequencee | Patient(s)f | |
|---|---|---|---|---|---|---|---|
| 5′ | 3′ | ||||||
| usRNA vRNAex | Ts5gag (3) | Sense | + | 1372 | 1397 | CAAGCAGCCATGCAAATGTTAAAAGA | 03, 04, 06-08, 13-16 |
| HIV-DNA | CAAGCAGCTATGCAGATGTTAAAAGA | 05 | |||||
| CAGGCAGCTATGCAAATGTTAAAAGA | 10 | ||||||
| CAGGCAGCTATGCAAATGTTAAAAGA | 11 | ||||||
| Boe3tq (3) | Probe | − | 1430 | 1405 | f-CTATCCCATTCTGCAGCTTCCTCATT-q | 03-08, 13, 15, 16 | |
| f-CCTGTCCCATTCTGCAGCTTCCTCATT-q | 10 | ||||||
| f-CCTGTCCCATTCTGCAGCTTCCTCATT-q | 11 | ||||||
| f-CCTATCCCATTCTGCAGCCTCCTCATT-q | 14 | ||||||
| Boe2 (3) | Antisense | − | 1488 | 1467 | TCCCCTTGGTTCTCTCATCTGG | 03, 05-08, 13 | |
| TCCCCTTGGTTCTCTCATCTGA | 04 | ||||||
| TCCCCTTGGTTCTCTCATCTGA | 10 | ||||||
| TCCCCTTGGTTCCCTTATCTGG | 11 | ||||||
| Skcc1b (46) | Antisense | − | 1513 | 1486 | TACTAGTAGTTCCTGCTATGTCACTTCC | 14-16 | |
| msRNA | Ts5allspl (19) | Sense | + | 5978 | 6001 | AAGAAGCGGAGACAGCGACGAAGA | 04-07 |
| AAGAAGCGAAGACAGCGACGAAGA | 03 | ||||||
| Mf84 (19, 50) | Sense | + | 6012 | 6045 | ACAGTCAGACTCATCAAGTTTCTCTATCAAAGCA | ||
| ACAGTAAGACTCATCAAGCTTCTCTATCAAAGCA | 08 | ||||||
| GCAGTGAAGATCATCAAAATCCTATATCAAAGCA | 10 | ||||||
| GCAATAAGGATCATCAAAATCCTATA | 11 | ||||||
| ACCGTCAGACTAATCAAGATTCTCTATCAAAGCA | 13 | ||||||
| GCAGTGAGGATCATCAAAATCCTATATCAAAGCA | 14 | ||||||
| ACAATCAGACTCATCAGGCTTCTCTATCAAAACA | 15 | ||||||
| ACAGTCAGATTCATCAAGTTTCTCTATCAAAGCA | 16 | ||||||
| mf2tq (19, 52) | Probe | − | 8421 | 8399 | f-TTCCTTCGGGCCTGTCGGGTCCC-q | 04, 07 | |
| f-TTCCTCCGGGCCTGTCGGGTTCCC-q | 03 | ||||||
| f-TTCCTCCGGGCCTGTCGGGTCCC-q | 05 | ||||||
| f-TTCCTTCGGGCCCGTCGGGTCCC-q | 06 | ||||||
| Mf226tq | Probe | + | 8397 | 8414 | f-AGGGGACCCGACAGGCCC-q | 08, 13, 15, 16 | |
| f-AGGGGTCTCGACAGGCCC-q | 10 | ||||||
| f-AGGGATCTCGACAGGCCC-q | 11 | ||||||
| f-AGGGGACCCGACAGGCTC-q | 14 | ||||||
| Mf83 (19, 50) | Antisense | − | 8459 | 8433 | GGATCTGTCTCTGTCTCTCTCTCCACC | 03, 06, 07, 13 | |
| GGATCTGCCGCTGTCTCTCTCTCCACC | 04 | ||||||
| GGATCTGTCTCTGTCTCTTTCTCCACC | 05 | ||||||
| TGATGTGTCTCTGTCTCTCTCTCCACC | 08 | ||||||
| TGATCTGTCTCTGTCTTGCTCTCCACC | 10 | ||||||
| CGATCTGCTTCTGTCTTGCTCTCCACC | 11 | ||||||
| GGATCTGTCTCTGCCTTGCTCTCCACC | 14 | ||||||
| GGATCTGTCTCTGTCTCTGTCCCCACC | 15 | ||||||
| GGATGTGTCTCTGTCTCTCTCTCCACC | 16 | ||||||
Primers are denominated according to internal nomenclature in the authors' laboratory and not necessarily by previously used designations in the indicated references.
Functions of oligonucleotides: sense, primer of positive polarity used for PCR; antisense, primer of negative polarity used for cDNA synthesis and PCR; probe, fluorogenic probe used for detection of genuine amplification products.
+, coding strand of the proviral genome; −, noncoding strand.
Numbering on the HXB2 genome according to the software provided by the Los Alamos HIV database (SEQUENCE LOCATOR; www.hiv.lanl.gov).
Sequences are given 5′ to 3′ from left to right. Underlined positions show deviation from the standard sequence (HXB2 or clade B consensus) which is indicated in bold letters. f, fluorescein moiety attached to the DNA probe; q, fluorescence quenching moiety attached to the DNA probe.
Primers were adjusted to isolates from the patient(s) listed.