TABLE 2.
Model oligonucleotide substrates
| Oligonucleotide | Left overlapa | 7-1-7 Consensus sitesa TGATAAT-ATTATCA TGATAAT-ATTATCA(L) TGATAAT-ATTATCA(R) | Right overlapa | Low-mobility complexb |
|---|---|---|---|---|
| (7-1-7)2c | 1 | CGCAGTCGATAATGATAATCATTATCAGTCGCG | 6 | ++ |
| 9-1-9 | 4 | AGTCGACAATGATAATCATTATCATTCGCGCGC | 4 | ++ |
| 8-1-8 | 3 | AGTCGACGATGATAATCATTATCATCCGCGCGC | 3 | + |
| 8-1-7 | 3 | AGTCGACGATGATAATCATTATCACCCGCGCGC | 2 | +/− |
| 7-1-7 | 2 | CGCAGTCAGTGATAATTATTATCAGTAGTCGCG | 3 | − |
| 6-1-6 | 2 | CGCAGTCAGCGATAATTATTATCGGTAGTCGCG | 2 | − |
| Two 6-mers | 2 | CGCAGTCAGCGATAATGATAATTGGTAGTCGCG | 2 | NA |
| 6-mer | NA | CGCAGTCAGCGATAATCGCCGCTGGTAGTCGCG | NA | NA |
| nsd | NA | CGCAGTCAGCAGCGGCAGCCGCAGGTAGTCGCG | NA | NA |
As in Table 1, (L) indicates the position of a possible overlapping 7-1-7 binding site to the left of the central aligned site and (R) indicates the position of a possible site to the right to the aligned site. The extents to which the aligned 7-1-7 motifs (bases in bold) also have an overlapping site to either the right or the the left were determined by tabulating the matches with the six additional bases that would contribute to the overlapping site. Sites with matches at four or more positions are indicated by boldface type. NA, not applicable, since the oligonucleotide lacks a central 7-1-7 (or related) motif and therefore does not form specific complexes.
The presence of the lower-mobility complex is indicated for each of the model oligonucleotides as observed in EMSA experiments (Fig. 2).
Note that the (7-1-7)2 DNA contains a perfect match with the 19-bp Fur box consensus sequence but contains a C instead of a T for the first base of the left 7-1-7 inverted repeat.
ns, nonspecific DNA fragment.