Table 1.

Sequences of primers and linkers used in this study

NameLocationSequence
Gene-specific primers used for in vivo footprinting
 Primer set A (noncoding strand)
  A1(bp −211 to −191)5′-TGTATGAAAGATCATGCCGA-3′
  A2(bp −200 to −180)5′-ATCATGCCGACCTAGGAGCCG-3′
  A3(bp −181 to −156)5′-CCACCGCCCCGTAAACCAGACAGA-3′
 Primer set B (coding strand)
  B1(bp 8 to −16)5′-AGCTCAATCGCCGTGGTCTTCGCAA-3′
  B2(bp −6 to −30)5′-CCGCTAACTCGACAGGGCCGGCATT-3′
  B3(bp −30 to −57)5′-TTATTAATTTATCAGCAGGTGAGGTCAG-3′
 Primer set C (coding strand)
  C1(bp 97 to 74)5′-TACCTGACCGCTGCCGGATAGCCG-3′
  C2(bp 84 to 60)5′-CCGGATAGCCGACCAGAAGGTCTCG-3′
  C3(bp 60 to 34)5′-GGGAGCAAGAGAGCTCAGGACCGA-3′
 Linkers
  15′-GCGGTGACCCGGGAGATCTGAATTC-3′
  25′-GAATTCAGATC-3′
Primers used for mutagenesis
 Vector primers
  15′-ACGGUUAUCCACAGAAUCA-3′
  25′-ACUGGAACAACACUCAACC-3′
 Universal primers
  15′-AUUCUGUGGAUAACCGUA-3′
  25′-AGUGUUGUUCCAGUTTGG-3′
Primers for CAT plasmid constructs
  1LTR 5′ primer5′-TGTATGAAAGATCATGCCGAC-3′
  2LTR 3′ primer5′-ATTGTTTGCCGGTCTCTCCT-3′