Oligo sequences used in this study
| Primers | Forward (5′-3′) | Reverse (5′-3′) |
| TLR9 | CGTCTTGAAGGCCTGGTGTTGA | CTGGAAGGCCTTGGTTTTAGTGA |
| β2Microglobulin | TGCTGTCTCCATGTTTGATGTATCT | TCTCTGCTCCCCACCTCTAAGT |
| HPV16E1 | CATAGAGATGCAGTACAGG | CTCACCCCGTATAACTC |
| HPV16E6 | CCCACAGGAGCGACCCAGAAAGTT | CCCATCTCTATATACTATGCATAAATCCC |
| HPV16E7 | As previously described (Mansour et al., 2007) | |
| NF-κB for ChIP | ||
| Site A | TGGGTCTGTACCTGTGTGTGCA | TTCATTCCCTCCATCCACCTC |
| Site B | TGGATGGCCCTGTTGAGAGGG | TAGCCCCTGGGCATTCTCCTG |
| Site C | CTGGAGAGCACTCAGGGGAAC | GTCACACTAGGTCCCTCCTC |
| Site D | AGGCCCTGCAGAACTCTGGAG | TCAGGCAGAGAGCAGGGAGA |
| Cloning | ||
| Site B | CCGCTAGCAGATCTGGGGTGGGAGGTTT | CTCGAGCCCCTGCTTGCAGTGATCGTG |
| Mutations TLR9 promoter of NF-κB sites | ||
| Site A | NFAF: AAGGGACTCTGGGCCCTCATCAGGCTTG | NFAR: CAAGCCTGATGAGGGCCCAGAGTCCCTT |
| Site B | NFBF: GAGACTTGGGGACTCGGTCAGGCAGAGGGA | NFBR: TCCCTCTGCCTGACCGAGTCCCCAAGTCTC |
| Site C | NFCF: ACA/GCG/GGT/GGA/CTT/GTC/CAT/AGG/GCC/TT | NFCR: AAGGCCCTATGGACAAGTCCACCCGCTGT |
| Site D | As previously described (Fathallah et al.) | |
| ERα site biotinylateda | TCAGGCAGAGGTTTCAGCACATC | GATGTGCTGAAACCTCTGCCTGA |
| NF-κB minimal promoter sites, annealing primers | CCGCTAGCGAGTTTCTCGAGCC | GGCGATCGCTCAAAGAGCTCGG |
| siRNA | ||
| HPV16E6E7 | UCCAUAUGCUGUAUGUGAU | |
| HPV16E7 | GCACACACGUAGACAUUCG | |
| IKKα | GCAGGCUCUUUCAGGGACA | |
| IKKβ | GGUGGAAGAGGUGGUGAGC | |
| NF-κB | As previously described (Hasan et al., 2005) | |
| Scramble | CGAAUGUCUACGUGUGUGC |
| Primers | Forward (5′-3′) | Reverse (5′-3′) |
| TLR9 | CGTCTTGAAGGCCTGGTGTTGA | CTGGAAGGCCTTGGTTTTAGTGA |
| β2Microglobulin | TGCTGTCTCCATGTTTGATGTATCT | TCTCTGCTCCCCACCTCTAAGT |
| HPV16E1 | CATAGAGATGCAGTACAGG | CTCACCCCGTATAACTC |
| HPV16E6 | CCCACAGGAGCGACCCAGAAAGTT | CCCATCTCTATATACTATGCATAAATCCC |
| HPV16E7 | As previously described (Mansour et al., 2007) | |
| NF-κB for ChIP | ||
| Site A | TGGGTCTGTACCTGTGTGTGCA | TTCATTCCCTCCATCCACCTC |
| Site B | TGGATGGCCCTGTTGAGAGGG | TAGCCCCTGGGCATTCTCCTG |
| Site C | CTGGAGAGCACTCAGGGGAAC | GTCACACTAGGTCCCTCCTC |
| Site D | AGGCCCTGCAGAACTCTGGAG | TCAGGCAGAGAGCAGGGAGA |
| Cloning | ||
| Site B | CCGCTAGCAGATCTGGGGTGGGAGGTTT | CTCGAGCCCCTGCTTGCAGTGATCGTG |
| Mutations TLR9 promoter of NF-κB sites | ||
| Site A | NFAF: AAGGGACTCTGGGCCCTCATCAGGCTTG | NFAR: CAAGCCTGATGAGGGCCCAGAGTCCCTT |
| Site B | NFBF: GAGACTTGGGGACTCGGTCAGGCAGAGGGA | NFBR: TCCCTCTGCCTGACCGAGTCCCCAAGTCTC |
| Site C | NFCF: ACA/GCG/GGT/GGA/CTT/GTC/CAT/AGG/GCC/TT | NFCR: AAGGCCCTATGGACAAGTCCACCCGCTGT |
| Site D | As previously described (Fathallah et al.) | |
| ERα site biotinylateda | TCAGGCAGAGGTTTCAGCACATC | GATGTGCTGAAACCTCTGCCTGA |
| NF-κB minimal promoter sites, annealing primers | CCGCTAGCGAGTTTCTCGAGCC | GGCGATCGCTCAAAGAGCTCGG |
| siRNA | ||
| HPV16E6E7 | UCCAUAUGCUGUAUGUGAU | |
| HPV16E7 | GCACACACGUAGACAUUCG | |
| IKKα | GCAGGCUCUUUCAGGGACA | |
| IKKβ | GGUGGAAGAGGUGGUGAGC | |
| NF-κB | As previously described (Hasan et al., 2005) | |
| Scramble | CGAAUGUCUACGUGUGUGC |
Other biotin-labeled oligo probes were generated using site B forward WT or mutated biotinylated primers and respective nonbiotinylated reverse primers. Probe DNA was amplified using the TLR9 promoter plasmid as a template.