Kinetic modeling of ensemble integration assay

The data of the strand transfer assays for the length dependence of integration (1.8, 2.7, 4.6, and 7.2 kbp plasmids) was globally fitted to the model depicted in Supplementary Fig. 4a. The fit used the means and SDs from three repeats for each plasmid length and minimized the error-weighted least-square deviation of the model from the data using the Levenberg-Marquardt algorithm implemented in the lsqnonlin function of Matlab (Mathworks). The fraction of active intasome, the rate of half-site integration (k_hs), and the rate of full-site integration (k_fs) were treated as fitting parameters that are the same for all plasmid length. In addition, the rates for TCC formation (k_on) were treated as four indepdenent fitting parameters for each plasmid length. The off-rate for dissociation of the TCC was initially fit, but found to be very small or negligible. Therefore, it was fixed to k_off = 10⁻¹⁰ min⁻¹ in the final analysis.