Relaxation rate per run and total relaxation rate for Topo I and Topo III. (A) Histogram showing the distribution of the relaxation rate per run. In all cases, Topo III has a faster relaxation rate per run than Topo I. In the case of negatively supercoiled DNA, Topo III is faster by a factor of ∼40. The inset shows the distribution of relaxation rate per run for negatively supercoiled DNA by Topo III. (B) Histogram showing the distribution of the total relaxation rate. Topo I has a faster total relaxation rate than Topo III, in agreement with bulk experiments. The inset shows the distribution of the total relaxation rate for negatively supercoiled DNA by Topo III. In all cases, shaded bars correspond to Topo I and white ones to Topo III. For mismatched substrates (marked by filled circles) Topo III relaxation was only observed in 20% of the experiments. The different substrates used are shown at the bottom, where -SC corresponds to negatively supercoiled DNA, and 12B, 12 M, 27B and 27 M correspond to the 12-bp and 27-bp bulged and mismatched substrates. In all cases, the differences observed between the two enzymes are significant as assessed by the P-value (P-value of 0.0001 for all compared pairs, except for the 12-bp mismatch in panel B, with a P-value of 0.02). The error bars shown correspond to the standard errors. Details on the number of events used for each histogram are found in Supplementary Table 1.