Table 3.
Primers for analysis of E1 and E2 gene disruption.
| Assay | Primers (5'-3') | TA | Nucleotide position | Amplicon size (bp) | ||
|---|---|---|---|---|---|---|
| HPV16 | E1a | forward: | CCATGGCTGATCCTGCAG | 61 °C | 863–1219 | 356 bp |
| reverse: | TCTCCTTTTTGCAGCTCT | |||||
| E1b | forward: | GACAGCGGGTATGGCAAT | 65 °C | 1254–1663 | 409 bp | |
| reverse: | CATTCCCCATGAACATGC | |||||
| E1c | forward: | AATAAATCAACGTGTTGCGATTGG | 65 °C | 1548–2084 | 536 bp | |
| reverse: | GTTTATAATGTCTACACATTGTTG | |||||
| E1d | forward: | GGATTGTGCAACAATGTG | 65 °C | 2072–2527 | 455 bp | |
| reverse: | TGGAGGGCATTTTAGTTG | |||||
| E1e | forward: | CAACTAAAATGCCCTCCA | 61 °C | 2529–2845 | 316 bp | |
| reverse: | CGCATGTGTTTCCAATAG | |||||
| E2a | forward: | CGAGGACAAGGAAAACGA | 65 °C | 2738–3189 | 451 bp | |
| reverse: | CTTGACCCTCTACCACAG | |||||
| E2b | forward: | GGTTTATATTATGTTCATGAAGG | 56 °C | 3220–3599 | 379 bp | |
| reverse: | TATGGGTGTAGTGTTACTATTACA | |||||
| E2c | forward: | GTAATAGTAACACTACACCCATA | 56 °C | 3596–3853 | 257 bp | |
| reverse: | GGATGCAGTATCAAGATTTG | |||||
| HPV18 | E1P1 | forward: | GGTGTGCATCCCAGCAGTAA | 59 °C | 888–1403 | 515 bp |
| reverse: | GCCGCCACTACATACATTGC | |||||
| E1P2 | forward: | GCGGCAATGTATGTAGTGGC | 59 °C | 1400–1908 | 508 bp | |
| reverse: | GCTGCAACACTACTTCGCAA | |||||
| E1P3 | forward: | TCAACCACCAAAATTGCGAAGT | 59 °C | 1877–2211 | 334 bp | |
| reverse: | TCGTTTTTGGGCTCGCCTAT | |||||
| E1P4 | forward: | GCAAACATTATAGGCGAGCCC | 59 °C | 2181–2546 | 365 bp | |
| reverse: | TGTCCAACACGTGGTCGTT | |||||
| E1P5 | forward: | GGTGGCCATGTTAGATGATGC | 59 °C | 2506–2895 | 389 bp | |
| reverse: | GATTTTGTCCTGCAACGCACT | |||||
| E2P1 | forward: | TCCAGATTAGATTTGCACGA | 61 °C | 2786–3192 | 407 bp | |
| reverse: | CAATTGTCTTTGTTGCCATC | |||||
| E2P2 | forward: | ATACAAAACCGAGGATTGGA | 61 °C | 3086–3388 | 303 bp | |
| reverse: | ACTTCCCACGTACCTGTGTT | |||||
| E2P3 | forward: | AACACAGGTACGTGGGAAGT | 61 °C | 3369–3739 | 371 bp | |
| reverse: | TTTCGCAATCTGTACCGTAA | |||||
| E2P4 | forward: | GACCTGTCAACCCACTTCT | 61 °C | 3598–3994 | 397 bp | |
| reverse: | ACATGGCAGCACACATACAT | |||||
| HPV45 | E1a | forward: | GGTGTAATGGCTGGTTCTTTGT | 55 °C | 881–1139 | 259 bp |
| reverse: | AATGGACTGTTTTCCTTGCTGC | |||||
| E1b | forward: | CAGTCCATTAGGGGAGCAGC | 57.5 °C | 1131–1775 | 645 bp | |
| reverse: | GCTGCAACACTACTTCGCAA | |||||
| E1c | forward: | AGCACATTGTTGCACGTACC | 57.5 °C | 1705–2144 | 440 bp | |
| reverse: | GGTCTCCAATCCCCACCTTC | |||||
| E1d | forward: | AAGGTGGGGATTGGAGACCC | 62 °C | 2126–2727 | 602 bp | |
| reverse: | AGGGATTCCTTCGGTGTCTG | |||||
| E1e | forward: | TTTGCACGAGGACGATGAAGA | 55 °C | 2685–2890 | 206 bp | |
| reverse: | CACCTGGTGGTTTAGTTTGGTAA | |||||
| E2a | forward: | GGACATGGTCCAGATTAGATTTGC | 55 °C | 2666–3068 | 403 bp | |
| reverse: | GCACGGTTTTACCGCCTTTT | |||||
| E2b | forward: | TACAGAACCGTCGCAGTGTT | 62 °C | 3025–3431 | 407 bp | |
| reverse: | TCTGGATGTGGGGTTTTGGG | |||||
| E2c | forward: | AGACAGCTACAACACGCCTC | 62 °C | 3359–3893 | 535 bp | |
| reverse: | TGCAGCACACATAAAGGCAC | |||||
Note. Bp, base pairs; primers covering E1 and E2 of HPV16 were designed by Vermont et al. (2007), and primers of E2 of HPV18 by Collins Constandinou-Williams et al. (2009).