Values of binding and dissociation rate constants
| Value | XPC | TFIIH | XPG | XPA | XPF/ ERCC1 | RPA | PCNA |
| Concentration (µM) | 0.140 | 0.360 | 0.440 | 1.110 | 0.170 | 1.110 | 1.110 |
| Damaged DNA | |||||||
| kon (µM−1s−1) | 0.008 (0.007; 0.011) | 1.6 (0.8; 4.5) | NA | NA | NA | NA | NA |
| koff (s−1) | 0.061 (0.007; 0.462) | 0.053 (0.004; 0.195) | NA | NA | NA | NA | NA |
| Kd (µM) | 7.8 | 0.03 | NA | NA | NA | NA | NA |
| Partially unwound DNA | |||||||
| kon (µM−1s−1) | 0.002 (0.001; 0.003) | 0.26 (0.11; 0.27) | 0.28 (0.19; 0.31) | 0.13 (0.12; 0.16) | 1.2 (1.1; 1.6) | 0.15 (0.11; 0.22) | NA |
| koff (s−1) | 0.007 (0.006; 0.008) | 0.012 (0.009; 0.016) | 0.015 (0.012; 0.015) | 1.04 (0.75; 1.30) | 0.01 (0.011; 0.014) | 2.6 (1.7; 3.6) | NA |
| Kd (µM) | 3.1 | 0.05 | 0.05 | 7.7 | 0.01 | 17 | NA |
| τ = 35 ± 30 min | |||||||
| Fully unwound DNA | |||||||
| kon (µM−1s−1) | 0.002 (0.001; 0.003) | 0.26 (0.11; 0.27) | 0.28 (0.19; 0.31) | 0.13 (0.12; 0.16) | 1.2 (1.1; 1.6) | 0.006 (0.006; 0.007) | NA |
| koff (s−1) | 0.007 (0.006; 0.008) | 0.012 (0.009; 0.016) | 0.015 (0.012; 0.015) | 1.04 (0.75; 1.30) | 0.01 (0.011; 0.014) | 0.021 (0.020; 0.022) | NA |
| Kd (µM) | 3.1 | 0.05 | 0.05 | 7.7 | 0.01 | 3.27 | NA |
| τ = 41 ± 36 min | |||||||
| Incised DNA | |||||||
| kon (µM−1s−1) | 0.22 (0.13; 0.26) | 0.0004 (0.0003; 0.010) | 0.001 (0.0004; 0.007) | 0.004 (0.004; 0.005) | 0.09 (0.07; 0.11) | 0.006 (0.006; 0.007) | 0.001 (0.001; 0.002) |
| koff (s−1) | 0.40 (0.21; 0.48) | 0.05 (0.04; 0.07) | 0.10 (0.04; 0.11) | 0.06 (0.05; 0.07) | 0.050 (0.040; 0.101) | 0.021 (0.020; 0.022) | 0.004 (0.004; 0.004) |
| Kd (µM) | 1.8 | 137 | 89 | 13 | 0.53 | 3.27 | 2.8 |
| τ = 41 ± 36 min | |||||||
| Resynthesized DNA | |||||||
| kon (µM−1s−1) | NA | NA | NA | 0.054 (0.054; 0.058) | NA | 0.08 (0.05; 0.10) | 0.010 (0.007; 0.010) |
| koff (s−1) | NA | NA | NA | 0.004 (0.004; 0.005) | NA | 0.04 (0.03; 0.05) | 0.002 (0.002; 0.002) |
| Kd (µM) | NA | NA | NA | 0.08 | NA | 0.51 | 0.19 |
| τ = 2.0 ± 0.7 h | |||||||
| Rechromatinized DNA | |||||||
| kon (µM−1s−1) | NA | NA | NA | NA | NA | 0.07 (0.06; 0.07) | 0.31 (0.25; 0.34) |
| koff (s−1) | NA | NA | NA | NA | NA | 0.04 (0.04; 0.05) | 0.05 (0.04; 0.05) |
| Kd (µM) | NA | NA | NA | NA | NA | 0.61 | 0.16 |
| τ = 2.2 ± 0.7 h | |||||||
| Value | XPC | TFIIH | XPG | XPA | XPF/ ERCC1 | RPA | PCNA |
| Concentration (µM) | 0.140 | 0.360 | 0.440 | 1.110 | 0.170 | 1.110 | 1.110 |
| Damaged DNA | |||||||
| kon (µM−1s−1) | 0.008 (0.007; 0.011) | 1.6 (0.8; 4.5) | NA | NA | NA | NA | NA |
| koff (s−1) | 0.061 (0.007; 0.462) | 0.053 (0.004; 0.195) | NA | NA | NA | NA | NA |
| Kd (µM) | 7.8 | 0.03 | NA | NA | NA | NA | NA |
| Partially unwound DNA | |||||||
| kon (µM−1s−1) | 0.002 (0.001; 0.003) | 0.26 (0.11; 0.27) | 0.28 (0.19; 0.31) | 0.13 (0.12; 0.16) | 1.2 (1.1; 1.6) | 0.15 (0.11; 0.22) | NA |
| koff (s−1) | 0.007 (0.006; 0.008) | 0.012 (0.009; 0.016) | 0.015 (0.012; 0.015) | 1.04 (0.75; 1.30) | 0.01 (0.011; 0.014) | 2.6 (1.7; 3.6) | NA |
| Kd (µM) | 3.1 | 0.05 | 0.05 | 7.7 | 0.01 | 17 | NA |
| τ = 35 ± 30 min | |||||||
| Fully unwound DNA | |||||||
| kon (µM−1s−1) | 0.002 (0.001; 0.003) | 0.26 (0.11; 0.27) | 0.28 (0.19; 0.31) | 0.13 (0.12; 0.16) | 1.2 (1.1; 1.6) | 0.006 (0.006; 0.007) | NA |
| koff (s−1) | 0.007 (0.006; 0.008) | 0.012 (0.009; 0.016) | 0.015 (0.012; 0.015) | 1.04 (0.75; 1.30) | 0.01 (0.011; 0.014) | 0.021 (0.020; 0.022) | NA |
| Kd (µM) | 3.1 | 0.05 | 0.05 | 7.7 | 0.01 | 3.27 | NA |
| τ = 41 ± 36 min | |||||||
| Incised DNA | |||||||
| kon (µM−1s−1) | 0.22 (0.13; 0.26) | 0.0004 (0.0003; 0.010) | 0.001 (0.0004; 0.007) | 0.004 (0.004; 0.005) | 0.09 (0.07; 0.11) | 0.006 (0.006; 0.007) | 0.001 (0.001; 0.002) |
| koff (s−1) | 0.40 (0.21; 0.48) | 0.05 (0.04; 0.07) | 0.10 (0.04; 0.11) | 0.06 (0.05; 0.07) | 0.050 (0.040; 0.101) | 0.021 (0.020; 0.022) | 0.004 (0.004; 0.004) |
| Kd (µM) | 1.8 | 137 | 89 | 13 | 0.53 | 3.27 | 2.8 |
| τ = 41 ± 36 min | |||||||
| Resynthesized DNA | |||||||
| kon (µM−1s−1) | NA | NA | NA | 0.054 (0.054; 0.058) | NA | 0.08 (0.05; 0.10) | 0.010 (0.007; 0.010) |
| koff (s−1) | NA | NA | NA | 0.004 (0.004; 0.005) | NA | 0.04 (0.03; 0.05) | 0.002 (0.002; 0.002) |
| Kd (µM) | NA | NA | NA | 0.08 | NA | 0.51 | 0.19 |
| τ = 2.0 ± 0.7 h | |||||||
| Rechromatinized DNA | |||||||
| kon (µM−1s−1) | NA | NA | NA | NA | NA | 0.07 (0.06; 0.07) | 0.31 (0.25; 0.34) |
| koff (s−1) | NA | NA | NA | NA | NA | 0.04 (0.04; 0.05) | 0.05 (0.04; 0.05) |
| Kd (µM) | NA | NA | NA | NA | NA | 0.61 | 0.16 |
| τ = 2.2 ± 0.7 h | |||||||
NA, not applicable. The values for the different repair proteins are arranged in columns for the different DNA repair intermediates to which they bind (rows). The dissociation constants Kd = koff/kon are also given. Reference parameter set and 90% confidence intervals (in parentheses) are shown. Nuclear concentration (in micromolars) of NER factors XPC, XPA, and XPG are based on previously described data (Araújo et al., 2001), whereas RPA and PCNA amounts are estimated to be 250,000 molecules per cell, and TFIIH and ERCC1-XPF were estimated at 65,000 and 50,000 molecules per cell, respectively, based on previous estimates (Houtsmuller et al., 1999; Moné et al., 2004). Concentrations are calculated assuming a nuclear volume of 0.3 pL.