Figure 4.
DNA twisting. The loop capture and release rates from the IF series of constructs are plotted as functions of: (i) the loop size [(A) and (C), respectively]; (ii) the change in torque [(B) and (D)]. Black circles denote data from the intact DNA substrates; blue triangles, the nicked IFn constructs; green squares, the gapped IFg constructs. For the loop release rates, the data is separated for positive and negative torque (filled and unfilled circles, respectively). The variations of the rates with torque (C and D) are fitted with an Arrhenius law: the best fits are shown as red lines in all four panels. Introducing a nick between the sites did not release any torque within the loop: the IFn constructs (blue triangles) behaved like the intact constructs. But, the introduction of a gap between the two sites released all torque effects: the rates with the IFg substrates were invariant with inter-site spacing [green squares (A) and (C), grey band shows the confidence intervals of a linear fit]. This data shows that loop capture is fastest when there is zero torque [grey band in (A) and (B)], but loop release rates are not necessarily minimized by the absence of torque [grey band in (C) and (D)]: the latter indicates that a limited amount of negative torque stabilizes the protein–protein synapse. Moreover, it also explains why the capture and release rates are out of phase with respect to the loop size [(A) and (C)]. The arrow in (C) marks the loop size at which there is zero torque on the protein–protein interface (see text).