Table 3.
The binding site sequences used in gel-shift experiments with the ZIF-MUT fusion peptides and the binding affinities obtained
| Binding site name | Binding site sequence* | Apparent
Kd, pM
|
|
|---|---|---|---|
| ZIF-F4-MUT | ZIF-serF-MUT | ||
| ZIF | GCGTGGGCG | 2,200 | 2,000 |
| ZM | GCGGACGCGGCGTGGGCG | 11 | 7 |
| Z1M | GCGGACGCGXGCGTGGGCG | 6 | 4 |
| Z2M | GCGGACGCGX2GCGTGGGCG | 7 | 6 |
| Z3M | GCGGACGCGX3GCGTGGGCG | 5 | 4 |
| Z4M | GCGGACGCGX4GCGTGGGCG | 13 | 3 |
| Z5M | GCGGACGCGX5GCGTGGGCG | 16 | 8 |
| Z6M | GCGGACGCGX6GCGTGGGCG | 17 | 7 |
| Z7M | GCGGACGCGX7GCGTGGGCG | 5 | 3 |
| Z8M | GCGGACGCGX8GCGTGGGCG | 5 | 6 |
| Z9M | GCGGACGCGX9GCGTGGGCG | 5 | 4 |
| Z10M | GCGGACGCGX10GCGTGGGCG | 4 | 3 |
*
Nonbound DNA bases in the target sequence are shown by a boldface X. The exact base composition of these gaps was found to have no significant effect on peptide affinity.