TABLE 2.
Restriction enzyme kinetic studies on nucleosomes containing poly(dA-dT) DNA
| Restriction enzyme | Region probed (approx bp from nucleosome end) | Keqconf (A16End)/ Keqconf (601.3) | Keqconf (A16Mid)/ Keqconf (601.3) |
|---|---|---|---|
| PstI | 6–11 | 2.15 ± 0.28 | |
| HindIII | 12–17 | 1.93 ± 0.77 | |
| AvaII | 18–22 | 1.76 ± 1.73 | 1.78 ± 0.34 |
| MspI | 22–25 | 1.41 ± 0.04 | 1.23 ± 0.26 |
| HaeIII | 26–29 | 2.24 ± 0.31 | 2.28 ± 1.08 |
| BamHI | 54–59 | 1.26 ± 0.28 | 1.77 ± 0.26 |
| TaqI | 66–69 | 0.95 ± 0.50 | 1.09 ± 0.09 |
| RsaI | 72–75 | 0.70 ± 0.43 | 0.99 ± 0.06 |
| HhaI | 76–79 | 1.28 ± 0.52 | 2.34 ± 0.27 |
| MseI | 93–96 | ND | 1.26 ± 0.30 |
| StyI | 100–105 | 1.51 ± 0.90 | 1.87 ± 1.09 |
| BfaI | 116–119 | 1.90 ± 0.97 | 1.87 ± 1.44 |
| PmlI | 128–133 | 1.58 ± ND | 1.99 ± ND |
| Avg | 1.46 ± 0.14 | 1.74 ± 0.12 |
a
Fold enhancements of DNA site accessibility (averages ± 1 standard deviation) for sites throughout each construct from multiple independent experiments. Fold enhancements for each independent experiment are obtained from ratios of best-fit rate constants for digestions of test nucleosomes (i.e., with any 601.3 derivative) versus control nucleosomes (i.e., with 601.3 DNA), scaled for the enzyme concentrations used (27–29). ND, not determined.