FIGURE 8.

Kinetic mechanisms for DNA polymerase incorporation and fitting of progress curves for incorporation of dCTP opposite G or N²-alkyl G. A, general mechanism. The mechanism without step 8 and the non-productive complex is termed the “minimal mechanism” in the text. Step 8 was used in fitting (Table 6). E, polymerase; D_n, DNA substrate; E*, conformationally modified polymerase; D_n+1, DNA extended by one base (product); E#, inactive polymerase complex; and PPi, pyrophosphate. Forward and reverse rate constants for each step were developed on the basis of simulations of pre-steady-state nucleotide incorporation reactions with unmodified substrates. Parts B–H, the values shown in Part A and the values of k₄, k₈, and k_–8 presented in Table 5 were used in fitting burst experiment progress curves for each of the templates (data points from Fig. 3).