Table 1.

Real Time PCR Primers and Reaction Conditions

NA Assessed	Primers	Sequence	Conc.	Conditions
Strong-Stop cDNA	AA55	5′-CTGCTAGAGATTTTCCACACTGAC-3′	200 nM	95°C, 3 min; 50X (93°C, 1 min;
	M667	5′-GGCTAACTAGGGAACCCACTG-3′		57°C, 1 min; 72°C, 1 min)
Y Chromosome DNA or Purified Standards	DYS14F	5′-CATCCAGAGCGTCCCTGGCTTCTGG-3′	200 nM	95°C, 3 min; 50X (93°C, 1 min;
	DYS14R	5′-TTCCCCTTTGTTCCCCAAA-3′		57°C, 1 min; 72°C, 1 min)
Genomic DNA w/wo	Alu2 (F)	5′-GCCTCCCAAAGTGCTGGGATTACAG-3′	100 nM	95°C, 3 min; 50X (93°C, 1 min; 55°C, 1 min; 72°C, 1 min)
Integrated Provirus or Purified Standards	Alu1 (R)	5′-TCCCAGCTACTGGGGAGGCTGAGG-3′
	LM667	5′-ATGCCACGTAAGCGAAACTCTGGCTAACTAGGGAACCCACTG-3′
Pre-amplified cDNA	AA55M	5′-GCTAGAGATTTTCCACACTGACTAA-3′	200 nM	95°C, 3 min; 50X (93°C, 1 min;
From Above	Lambda T	5′-ATGCCACGTAAGCGAAACTCT-3′		57°C, 1 min; 72°C, 1 min)
HIV mRNA Full Length	La 8.1	5′- CTGAAGCGCGCACGGCAA-3′	200 nM	50°C 10 min, 95°C 3 min, (94°C 1min, 56°C 1 min, 72°C 1 min)
Transcript	La 9	5′- GACGCTCTCGCACCCATCTC-3′		× 40 cycles, 4°C 10 min
HIV mRNA Multiply-Spliced Transcripts	P659	5′- GACTCATCAAGTTTCTCTATCAAA-3′	200 nM	50°C 10 min, 95°C 3 min, (94°C 1min, 56°C 1 min, 72°C 1 min)
	P413Mod	5′- AGTCTCTCAAGCGGTGGT-3′		× 40 cycles, 4°C 10 min
Genomic β-Globin or Purified Standards	β-GlobinF	5′CCCTTGGACCCAGAGGTTCT-3′	200 nM	95°C, 3 min; 50X (93°C, 1 min;
	β-GlobinR	5′-CGAGCACTTTCTTGCCATGA-3′		55/57 °C, 1 min; 72°C, 1 min)