TABLE 6.
Kinetic modeling of pre-steady-state rate constants in a DNA polymerase mechanism
Indicated rates and errors were estimated using the program Dynafit. See Fig. 8A for mechanism, Fig. 8 (B–H) for fits to progress curves, and supplemental Table S5 for Dynafit script and sample results.
|
Oligonucleotide base
|
EDN⇆XDN, k4
|
XDN⇆ODN
|
k8/k4
|
|
|---|---|---|---|---|
| k8 | k-8 | |||
| s-1 | s-1 | s-1 | ||
| G | 3.2 ± 0.7 | 2.1 ± 1.2 | 0.07 ± 0.19 | 0.66 |
| N2-MeG | 6.1 ± 0.6 | 1.4 ± 0.2 | 10-5 | 0.23 |
| N2-EtG | 1.6 ± 0.2 | 0.96 ± 0.23 | 0.053 ± 0.022 | 0.60 |
| N2-IbG | 0.18 ± 0.01 | 0.14 ± 0.02 | 0.025 ± 0.004 | 0.78 |
| N2-BzG | 0.40 ± 0.03 | 0.52 ± 0.05 | 10-5 | 1.3 |
| N2-NaphG | 0.15 ± 0.02 | 0.32 ± 0.10 | 0.06 ± 0.015 | 2.1 |
| N2-AnthG | 0.21 ± 0.01 | 1.0 ± 0.1 | 0.0070 ± 0.0030 | 4.8 |