Table 2.
Fitting parameters from thermodynamic DNA looping modela
| Strain |
spoptimal (bp) |
Capp (×10−19 erg cm) |
hr (bp/turn)b |
Kmax |
KNSLb |
Papp (bp)b |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| −IPTG | +IPTG | −IPTG | +IPTG | −IPTG | +IPTG | −IPTG | +IPTG | −IPTG | +IPTG | −IPTG | +IPTG | |
| WT+vec | 78.7 ± 0.3 | 79.3 ± 0.4 | 0.69 ± 0.13 | 0.89 ± 0.38 | 11.6 ± 0.3 | 11.0 ± 0.5 | 211 ± 103 | 2.5 ± 0.7 | (20.2) ± 21.0 | (0) ± 0.4 | (0) ± 188 | (238) ± 205 |
| ΔHU+vec | 76.8 ± 0.2 | 77.2 ± 1.0 | 0.66 ± 0.10 | 0.23 ± 0.08 | 11.1 ± 0.3 | (9.1) ± 1.2 | 65 ± 12 | 1.4 ± 0.4 | 8.8 ± 5.6 | (0) ± 0.8 | (10.4) ± 91.6 | (219) ± 304 |
| ΔHU+1327 | 77.0 ± 0.2 | 79.1 ± 2.3 | 0.53 ± 0.04 | 0.21 ± 0.13 | 11.6 ± 0.4 | (10.3) ± 2.5 | 113 ± 32 | 0.9 ± 0.3 | (0) ± 15 | (0) ± 0.7 | (160) ± 160 | (276) ± 376 |
| ΔHU+1328 | 76.7 ± 0.5 | 78.0 ± 1.4 | 0.30 ± 0.04 | 0.22 ± 0.09 | 11.0 ± 0.7 | (8.9) ± 1.5 | 171 ± 35 | 1.8 ± 0.7 | (0) ± 166 | (0) ± 0.8 | (114) ± 229 | (359) ± 398 |
| ΔHU+1200 | 78.7 ± 0.6 | 80.2 ± 0.9 | 0.32 ± 0.04 | 0.33 ± 0.12 | 12.9 ± 0.9 | 10.5 ± 1.1 | 87 ± 23 | 1.2 ± 0.4 | (0) ± 80 | (0) ± 0.5 | (168) ± 314 | (252) ± 330 |
| ΔHU+1299 | 78.2 ± 0.6 | 78.5 ± 1.2 | 1.21 ± 1.00 | 0.24 ± 0.11 | 13.2 ± 1.0 | (8.5) ± 1.3 | 112 ± 33 | 1.2 ± 0.5 | 62.5 ± 12.3 | (0) ± 2.4 | (8.1) ± 346 | (85.5) ± 497 |
| ΔHU+1492 | 77.1 ± 0.4 | 79.0 ± 1.5 | 0.42 ± 0.05 | 0.24 ± 0.10 | 12.0 ± 0.6 | (10.0) ± 1.5 | 108 ± 25 | 2.2 ± 0.7 | (0) ± 41 | (0) ± 0.8 | (90.4) ± 154 | (284) ± 320 |
| ΔHU+1493 | 76.7 ± 0.3 | 83.0 ± 0.9 | 0.55 ± 0.06 | 0.29 ± 0.08 | 11.9 ± 0.4 | (8.1) ± 0.6 | 103 ± 23 | 2.2 ± 1.0 | (3) ± 21 | (0) ± 1.2 | (22.0) ± 121 | (307) ± 442 |
aIndicated errors are 95% confidence limits. The values and ranges for Kmax, KNSL and Papp are fit only to expression data E+IPTG and E − IPTG. The values and ranges for spoptimal, Capp, and hr are fit to E+IPTG, E − IPTG and the repression ratio RR simultaneously, with Kmax, KNSL, and Papp held fixed.
bParentheses indicate a large error estimate, making the parameter value unreliable. However, trends ±IPTG are robust: upon induction spoptimal increases, Capp decreases, hr decreases, Kmax decreases, KNSL decreases or is negligible and Papp increases. When Capp is less than about 0.3, torsional oscillations are so small that hr cannot be estimated reliably.