Table 2

Primer sequences and PCR conditions

Target

Primer

Sequences (5'-3')

PCR conditions

Integrated HIV-1

DNA^a

• First round PCR

L-M667

ATGCCACGTAAGCGAAACTCTGGCTAACTAGGGAACCCACTG

95°C, 8 min and 95°C, 10 s, 60°C, 10 s, 72°C, 170 s for 12 cycles

Alu 1

TCCCAGCTACTGGGGAGGCTGAGG

Alu 2

GCCTCCCAAAGTGCTGGGATTACAG

• Second round PCR

Lambda T

ATGCCACGTAAGCGAAACT

95°C, 8 min and 95°C, 10 s, 60°C, 10 s, 72°C, 9 s for 40 cycles

AA55M

GCTAGAGATTTTCCACACTGACTAA

Linear HIV DNA^a

MH531

TGTGTGCCCGTCTGTTGTGT

95°C, 8 min and 95°C, 10 s, 60°C, 10 s, 72°C, 6 s for 40 cycles

MH532

GAGTCCTGCGTCGAGAGAGC

2-LTR circle^a

HIV F

GTGCCCGTCTGTTGTGTGTGACT

95°C, 8 min and 95°C, 10 s, 60°C, 10 s, 72°C, 10 s for 40 cycles

HIV R

ACTGGTACTAGCTTGTAGCACCATCCA

U5-U3 RNA^a

HIV F

GTGCCCGTCTGTTGTGTGTGACT

95°C, 2 min and 95°C, 5 s, 60°C, 10 s, 72°C, 10 s for 40 cycles

HIV R

ACTGGTACTAGCTTGTAGCACCATCCA

Gag

For

CCCATAGTGCAGAACATCCA

50°C, 2 min, 95°C, 2 min, and 95°C, 15s and 60°C, 30s, for 50 cycles

Rev

GGGCTGAAAGCCTTCTCTTC

Singly spliced^b

M669

GTGTGCCCGTCTGTTGTGTGACTCTGGTAAC

50°C, 2 min, 95°C, 2 min, and 95°C, 15s and 60°C, 30s, for 50 cycles

La 23

GCCTATTCTGCTATGTCGACACC

Multiply spliced HIV RNA^a

P659

GACTCATCAAGTTTCTCTATCAAA

95°C, 4 min and 95°C, 5 s, 54°C, 10 s, 72°C, 8 s for 40 cycles

P413MOD

AGTCTCTCAAGCGGTGGT

Unspliced HIV RNA^a

La 9

GACGCTCTCGCACCCATCTC

95°C, 2 min and 95°C, 10 s, 60°C, 40 s for 40 cycles

La 8.1

CTGAAGCGCGCACGGCAA

β-actin

Actin F

ATGGCCACGGCTGCTTCCAGC

95°C, 15 s, 55°C, 30 s, 72°C, 15 s for 30 cycles

Actin R

CATGGTGGTGCCGCCAGACAG

GAPDH

GAPDH F

GAGTCAACGGATTTGGTCGT

95°C, 15 s, 60°C, 30 s, 72°C, 15 s for 30 cycles

GAPDH R

TTGATTTTGGAGGGATCTCG

^a Primer sequences and PCR conditions were modified from [40]

^b Primer sequences and PCR conditions were modified from [74]

Vacharaksa et al. Retrovirology 2008 5:66   doi:10.1186/1742-4690-5-66