Table S1.
Sequences of p53 REs studied by EMSA experiments
| Name* | Sequence* | Dimer KD (nM)†,‡ | Dimer equivalent specific tetramer KD (nM)‡,§ | Cooperativity of the specific tetramer‡,¶ |
| GGG-GGG | cGGGCATGCCCGGGCATGCCCtg | 151 (30) | 6 (1) | 543 (74) |
| GGG-ta-GGG | cGGGCATGCCCtaGGGCATGCCCt | 172 (48) | 7 (1) | 535 (177) |
| GGG-(ta)2-GGG | cGGGCATGCCCtataGGGCATGCCCt | 216 (36) | 9 (2) | 542 (81) |
| GGG-(ta)3-GGG | cGGGCATGCCCtatataGGGCATGCCCt | 350 (46) | 16 (2) | 486 (67) |
| GGG-(ta)4-GGG | cGGGCATGCCCtatatataGGGCATGCCCt | 533 (60) | 24 (1) | 478 (48) |
| GGG-(ta)5-GGG | cGGGCATGCCCtatatatataGGGCATGCCCt | 450 (27) | 18 (1) | 656 (68) |
| GGG-(ta)6-GGG | cGGGCATGCCCtatatatatataGGGCATGCCCt | 409 (56) | 18 (1) | 538 (89) |
| GGG-(ta)7-GGG | cGGGCATGCCCtatatatatatataGGGCATGCCCt | 530 (68) | 28 (1) | 368 (62) |
| GGG-(ta)8-GGG | cGGGCATGCCCtatatatatatatataGGGCATGCCCt | 643 (116) | 37 (4) | 298 (56) |
| GGG-(ta)9-GGG | cGGGCATGCCCtatatatatatatatataGGGCATGCCCt | 627 (116) | 36 (3) | 292 (61) |
| GGG-(ta)10-GGG | cGGGCATGCCCtatatatatatatatatataGGGCATGCCCt | 311 (49) | 16 (1) | 449 (120) |
| N20(ta)5-GGG | cgcgcagtagggaggattcgatatatatataGGGCATGCCCt | 214 (34) | ||
| GGG-(ta)5N20 | cGGGCATGCCCtatatatatagaggattcgacgcgcagtagg | 220 (17) | ||
| N10GGG-GGGN10 | ccagagacaccGGGCATGCCCGGGCATGCCCgaagaggaaat | 230 (40) | 8 (1) | 945 (202) |
| N5GGG-(ta)5-GGGN5 | gacaccGGGCATGCCCtatatatataGGGCATGCCCgaagag | 481 (56) | 20 (1) | 596 (111) |
| GGG HS# | tggttgcGGGCATGCCCtgggta | |||
| CHMP4c | gAAACAAGCCCagtagcagcagctgctccGAGCTTGCCCa | |||
| CHMP4c RHS‖ | gcggaggcgatagtagcagcagctgctccGAGCTTGCCCa | 201 (26) | ||
| CHMP4c LHS‖ | gAAACAAGCCCagtagcagcagctgctccgcggaggcgta | 289 (24) | ||
| PTEN | gGAGCAAGCCCcaggcagctacactGGGCATGCTCg | |||
| PTEN RHS‖ | gcggaggcgtgcaggcagctacactGGGCATGCTCg | 151 (9) | ||
| PTEN LHS‖ | gGAGCAAGCCCcaggcagctacactgcggaggcgtg | 174 (10) |
The sequences are embedded in the stems of hairpin constructs with a 5-bp loop (21). The specific sites are shown in uppercase bold letters; spacer sequences are in lowercase underlined; nonspecific sites flanking the specific and spacer sites are in lowercase italics.
KD values of the p53 dimers bound to the specific sites.
The values are averages of four to eight independent experiments conducted with each sequence; the values in parentheses are the SEMs.
Dimer-equivalent tetramer KD is derived from the square root of Ka3, that is, the macroscopic specific tetramer value in Table 1. This KD and cooperativity cannot be derived for the hemispecific complex because Ka2 is composed of two different dimers, with binding constants k1 and k2. They cannot be computed for the natural REs either because the gel pattern of these REs was composed of a single bound tetrameric complex, and therefore the binding constant is a weighted average of specific and hemispecific values.
See definitions in SI Materials and Methods.
HS is half site, that is, a DNA binding site with a single specific half-site. This sequence is from Jordan et al. (31).
Right half-site (RHS) and left half-site (LHS) incorporate the specific right-handed and left-handed half-site decamer, respectively (uppercase bold), and the corresponding DNA spacer (lowercase underlined); nonspecific sequences were added to make the total length identical to that of the full site.