Table 1. Steady-state kinetic efficiencies for single-nucleotide insertions by DNA Pol I (Klenow fragment, exonuclease-deficient) with variably sized template bases.
dNTP | Template base | Vmax, %·min–1 | KM, μM | Efficiency, Vmax/KM | Relative efficiency |
---|---|---|---|---|---|
dATP | H | 0.90 ± 0.18 | 20 ± 2 | 4.5 × 104 | 3.5 × 10–3 |
F | 24 ± 3 | 9.4 ± 2.9 | 2.6 × 105 | 2.0 × 10–1 | |
L | 27 ± 5 | 3.3 ± 2.8 | 8.2 × 106 | 6.5 × 10–1 | |
B | 12 ± 1 | 21 ± 5 | 5.7 × 105 | 4.4 × 10–2 | |
I | 1.3 ± 0.2 | 26 ± 11 | 5.0 × 104 | 3.8 × 10–3 | |
T | 24 ± 1 | 1.9 ± 0.5 | 1.3 × 107 | 1 | |
dGTP | H | 0.025 ± 0.007 | 600 ± 210 | 4.2 × 101 | 3.2 × 10–6 |
F | 0.0071 ± 0.0006 | 36 ± 12 | 2.0 × 102 | 1.5 × 10–5 | |
L | 0.029 ± 0.007 | 190 ± 90 | 1.5 × 102 | 1.2 × 10–5 | |
B | 0.023 ± 0.005 | 220 ± 100 | 1.0 × 102 | 7.7 × 10–6 | |
I | 0.017 ± 0.001 | 58 ± 18 | 2.9 × 102 | 2.2 × 10–5 | |
T | 0.41 ± 0.15 | 56 ± 34 | 7.3 × 103 | 5.6 × 10–4 | |
dCTP | H | 0.031 ± 0.006 | 100 ± 60 | 3.1 × 102 | 2.4 × 10–5 |
F | 0.071 ± 0.011 | 33 ± 11 | 2.2 × 103 | 1.7 × 10–4 | |
L | 0.021 ± 0.003 | 25 ± 13 | 8.4 × 102 | 6.5 × 10–5 | |
B | 0.038 ± 0.005 | 79 ± 33 | 4.8 × 102 | 3.7 × 10–5 | |
I | 0.036 ± 0.001 | 20 ± 8 | 1.8 × 103 | 1.4 × 10–4 | |
T | 0.022 ± 0.006 | 46 ± 28 | 4.8 × 102 | 3.7 × 10–5 | |
dTTP | H | 0.062 ± 0.022 | 61 ± 37 | 1.0 × 103 | 7.7 × 10–5 |
F | 0.12 ± 0.03 | 22 ± 13 | 5.5 × 103 | 4.2 × 10–4 | |
L | 0.13 ± 0.04 | 18 ± 18 | 7.2 × 103 | 5.5 × 10–4 | |
B | 0.20 ± 0.03 | 37 ± 12 | 5.4 × 103 | 4.2 × 10–4 | |
I | 0.085 ± 0.037 | 48 ± 39 | 1.8 × 103 | 1.4 × 10–4 | |
T | 0.012 ± 0.004 | 38 ± 38 | 3.2 × 102 | 2.5 × 10–5 |
The template contained variably sized thymidine analogs. The kinetics were measured in a buffer containing 5 mM template–primer DNA, 0.005 or 0.1 unit/ml enzyme, 50 mM Tris-HCl buffer (pH 7.5), 10 mM MgCl2, 1 mM dithiothreitol, and 50 mg/ml bovine serum albumin at 37°C. Vmax was normalized to the lowest enzyme concentration used. Relative efficiency is relative to insertion of dATP opposite T.