Table 1. Oligodeoxynucleotides used during protein–DNA binding and methylation studies.
Oligonucleotide | Sequence (5′→3′) (top strand) |
---|---|
Zf | TTCCATGGAGACGCAGAAGCCCTTCAGTTCCAG |
ZfHhaI | GATGGCGAGGGC*GCCTTCCATGGAGACGCAGAAGCCCTTCAGCGGCCA |
ZfHpaII (Sep16) | GATGGCGAGGCC*GGCACACATGGAGACGCAGAAGCCCTTCAGCGGCCA |
HhaI | GGGATGGCCAGGGCGCCTTCCATGGAGAC |
HpaII | GATGGCGAGGCCGGCTTCCATGGAGACGCAGGTGAGTTCCTCACGCCA |
HpaII* | GTACGAGCAGCTCCCGGGTCAGTCTGCCTA |
Non-Sp | GCTGATTGCGAGGGTACCTTCCATGTAACTATTCTCTAACTTCAGG |
ZhpaII | GATGGCGAGGCCGGAAGCCCTTCAGCGGCCA |
Sep 2 | GATGGCGAGGCCGGCAGAAGCCCTTCAGCGGCC |
Sep 5 | GATGGCGAGGCCGGACGCAGAAGCCCTTCAGCGGCCA |
Sep 6 | GATGGCGAGGCCGGGACGCAGAAGCCCTTCAGCGGCCA |
Sep 11 | GATGGCGAGGCCGGATGGAGACGCAGAAGCCCTTCAGCGGCC |
Sep 17 | GATGGCGAGGCCGGTGTGCTGTAGCTACGCAGAAGCCCTTCAGCGGCCA |
Sep 22 | GATGGCGAGGCCGGTGTGCTGTAGCTGGAGGACGCAGAAGCCCTTCAGCGGCCA |
Sep 25 | GCTCATCCACTGCGCACTCATGTCAGACTACCCGGTGTGCTGTAGCTACTAAGTGACGCAGAAGCCCCTCAGTGC |
Sep 33 | GCTGCTCATCCATCCCGGCGCTTACTGGTGTAGCTAAGTCTAAGTGACGCAGAAGCCCCTCAGTGC |
Sep 39 | GCTCATCCACTCCCGGTGTCAGACTAGCGCTGTCTGTAGCTACTAAGTGACGCAGAAGCCCCTCAGTGC |
Sep 44 | GCTCATCCACTCCCGGACTCATGTCAGACTAGCGCTGTGCTGTAGCTACTAAGTGACGCAGAAGCCCCTCAGTGC |
Both the C5-Mtase and zinc finger recognition sites are underlined. ZfHhaI and ZfHpaII were also synthesised with 5-methyl-2′-deoxycytosine at the target cytosine in the C5-Mtase recognition site. The target base is asterisked in the respective sequences. Where indicated in the text, 5-methyl-2′-deoxycytosine was also present in the bottom strand at the corresponding symmetrically opposite target cytosine. [Only the top (5′→3′) strands are shown.] Base separation between subsites is measured from (and includes) the target cytosine in the HpaII site up to the first base before the zinc finger site.