Figure 2.

Estimation of Cutting and Repair Rates

(A–C) Representative time series traces of the intact (A), broken (B), and indel (C) fractions. Measured data (dots) are overlaid with the ODE model fit (solid lines). The percentage of intact and indel traces are relative to the total. The broken fraction is estimated by the model on the basis of the intact and indel measurements. τ indicates time of the largest amount of broken DNA.

(D) Distributions of rate constants from 7 independent experiments (values indicate mean ± SD).

(E) Estimate of the upper confidence bound of the proportion of perfect repair. Fitting residual errors are shown for various fixed k_p/(k_p+k_m) ratios (7 combined time series). Black dashed line marks the optimal fit; red dashed line marks the k_p/(k_p+k_m) ratio above which the fit becomes significantly worse than the optimal fit (p < 0.1; one-sided F-test). This corresponds to k_p/(k_p+k_m) = 0.28. For each k_p/(k_p+k_m) ratio, k_c,max and k_m were adjusted to produce the best fit.

(F) Examples of model fitting with various combinations of k_p and k_m forced to values that would correspond to models of rapid cycling of cutting and perfect repair (dashed curves). Green dots are measured values; green curve shows unrestrained optimal fit.