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. 2000 Mar;74(6):2489–2501. doi: 10.1128/jvi.74.6.2489-2501.2000

TABLE 1.

Overlapping oligonucleotides that completely represent the 5′-LCR-MAR and the E6-MARa

Name Genomic position Nucleotide sequence
LCR-1 7132–7162 5′-gatccTAAACGCAAAAAACGTAAGCTGTAAGTATTGa-3′
LCR-2 7147–7177 5′-gatccTAAGCTGTAAGTATTGTATGTATGTTGAATTa-3′
LCR-3 7163–7193 5′-gatccTATGTATGTTGAATTAGTGTTGTTTGTTGTGa-3′
LCR-4 7178–7208 5′-gatccAGTGTTGTTTGTTGTGTATATGTTTGTATGTa-3′
LCR-5 7194–7224 5′-gatccTATATGTTTGTATGTGCTTGTATGTGCTTGTa-3′
LCR-6 7209–7239 5′-gatccGCTTGTATGTGCTTGTAAATATTAAGTTGTAa-3′
LCR-7 7225–7255 5′-gatccAAATATTAAGTTGTATGTGTGTTTGTATGTAa-3′
LCR-8 7240–7270 5′-gatccTGTGTGTTTGTATGTATGGTATAATAAACACa-3′
LCR-9 7256–7286 5′-gatccTGGTATAATAAACACGTGTGTATGTGTTTTTa-3′
LCR-10 7271–7301 5′-gatccGTGTGTATGTGTTTTTAAATGCTTGTGTAACa-3′
LCR-11 7287–7317 5′-gatccAAATGCTTGTGTAACTATTGTGTCATGCAACa-3′
LCR-12 7302–7332 5′-gatccTATTGTGTCATGCAACATAAATAAACTTATTa-3′
LCR-13 7318–7348 5′-gatccATAAATAAACTTATTGTTTCAACACCTACTAa-3′
LCR-14 7333–7363 5′-gatccGTTTCAACACCTACTAATTGTGTTGTGGTTAa-3′
LCR-15 7349–7379 5′-gatccATTGTGTTGTGGTTATTCATTGTATATAAACa-3′
LCR-16 7364–7394 5′-gatccTTCATTGTATATAAACTATATTTGCTACATCa-3′
LCR-17 7380–7410 5′-gatccTATATTTGCTACATCCTGTTTTTGTTTTATAa-3′
LCR-18 7395–7425 5′-gatccCTGTTTTTGTTTTATATATACTATATTTTGTa-3′
LCR-19 7411–7441 5′-gatccTATACTATATTTTGTAGCGCCAGCGGCCATTa-3′
LCR-20 7426–7456 5′-gatccAGCGCCAGCGGCCATTTTGTAGCTTCAACCGa-3′
LCR-21 7442–7472 5′-gatccTTGTAGCTTCAACCGAATTCGGTTGCATGCTa-3′
E6-1 104–143 5′-ATGTTTCAGGACCCACAGGAGCGACCCAGAAAGTTACCAC-3′
E6-2 134–173 5′-AAGTTACCACAGTTATGCACAGAGCTGCAAACAACTATAC-3′
E6-3 164–203 5′-ACAACTATACATGATATAATATTAGAATGTGTGTACTGCA-3′
E6-4 194–233 5′-GTGTACTGCAAGCAACAGTTACTGCGACGTGAGGTATATG-3′
E6-5 224–263 5′-AGGTATATGACTTTGCTTTTCGGGATTTATGCATAGTATA-3′
E6-6 254–293 5′-GCATAGTATATAGAGATGGGAATCCATATGCTGTATGTGA-3′
E6-7 284–313 5′-CTGTATGTGATAAATGTTTAAAGTTTTATTCTAAAATTAG-3′
E6-8 314–343 5′-CTAAAATTAGTGAGTATAGACATTATTGTTATAGTTTGTA-3′
E6-9 344–373 5′-ATAGTTTGTATGGAACAACATTAGAACAGCAATACAACAA-3′
E6-10 374–403 5′-AATACAACAAACCGTTGTGTGATTTGTTAATTAGGTGTAT-3′
E6-11 404–433 5′-TTAGGTGTATTAACTGTCAAAAGCCACTGTGTCCTGAAGA-3′
E6-12 434–463 5′-GTCCTGAAGAAAAGCAAAGACATCTGGACAAAAAGCAAAG-3′
E6-13 464–493 5′-AAAAGCAAAGATTCCATAATATAAGGGGTCGGTGGACCGG-3′
E6-14 494–523 5′-GGTGGACCGGTCGATGTATGTCTTGTTGCAGATCATCAAG-3′
E6-15 524–553 5′-GATCATCAAGAACACGTAGAGAAACCCAGCTGTAATCATG-3′
a

These oligonucleotides span genomic positions 7132 to 7472 and 104 to 553, as indicated. The 5′-LCR-MAR is represented by 31-mers that overlap by 15 nucleotides, and the E6-MAR is represented by 40-mers with a 10-nucleotide overlap. In the case of the 5′-LCR-MAR, the nucleotides represented by lowercase letters were added to create artificial restriction sites for experiments unrelated to this study. For this research, they were used for radioactive labeling by the alpha deoxynucleotides and Klenow polymerase. Double-stranded E6 oligonucleotides were blunt ended and labeled with gamma deoxynucleotides and polynucleotide kinase.