Fig. 4.

Effect of DNA bridging restriction enzymes on 〈z〉 and 〈Δz²〉 in MT. (a) Time traces for z and σ_z = (〈Δz²〉)^1/2 measured in MT before and after addition of restriction enzymes at time t = 0. The restriction enzymes used are indicated on the left. Data for z are raw data recorded at 1 kHz. The standard deviation σ_z(t) was computed from z(t) using 1 s intervals. The histograms show the distribution of data points before (dashed lines) and after (solid lines) introduction of the proteins. (b) Change in mean extension Δ〈z〉 after protein binding as a function of expected loop length ΔL (Table 1). (c) Change in extension variance Δ〈Δz²〉 after protein binding vs. ΔL. The data in (b) and (c) are from at least five independent measurements for each enzyme. We quantified 〈Δz²〉 using the mean of the variance distributions. Black dots are individual measurements, colored circles and error bars the mean ± std over the independent measurements. The data show no substantial change in 〈z〉 and a drop in 〈Δz²〉 proportional to ΔL in agreement with Eq. (6), which is shown as a dashed line that is not a fit, but obtained from extrapolation of the experimental data (Fig. S6). A fraction of the experimental data points for the enzyme SacII deviate from the expected behavior (gray dots; excluded from further analysis), possibly indicating an alternative binding mode. All data shown were obtained at f = 0.5 pN and σ = 0.04.