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. 2022 Jan 25;11:e67021. doi: 10.7554/eLife.67021

Figure 6. Calculated average DNA-crossing angles for supercoils and braids, as a function of force.

The average DNA-crossing angle in positive and negative supercoils (+ sc [ink] and -sc [light blue], respectively) were calculated as described in Neukirch and Marko, 2011. The temperature was 293 K, the DNA persistence length was 50 nm and the monovalent salt concentration was 100 mM. The average DNA-crossing angles in positive and negative braids (+ braid [red] and -braid [dark blue], respectively) were calculated as described in Charvin et al., 2005. The temperature, DNA persistence length and monovalent salt concentration were the same as for supercoils. DNA duplex spacing was 600 nm, DNA-crossing number was eight and the DNA was 5080 bp long. In both the supercoil and braiding calculations, variables were set to mirror experimental conditions as close as possible. The horizontal grey line represents 90° and the dotted black line represents the topo VI DNA-crossing angle preference (α0 ≈ 87.5°).

Figure 6—source data 1. Source data is in the file Figure 6.

Figure 6.

Figure 6—figure supplement 1. Effect of force on the braid unlinking and supercoil relaxation activity of topo VI.

Figure 6—figure supplement 1.

(A) The average rate of positive (red, N tethers across all data points = 28) and negative (blue, N tethers across all data points = 22) braid unlinking (events min–1) (± SEM), plotted against force. (B) The average dwell times (s) between unlinking events for positive (red, N dwell times across all data points = 75) and negative (blue, N dwell times across all data points = 56) braids (± SEM), plotted against force. (C) The average processive burst rate (events min–1) for positive (red, N burst events across all data points = 80) and negative (blue, N burst events across all data points = 44) braid unlinking (± SEM), plotted against force. (D) The average step size (events burst–1) for positive (red, N = 92) and negative (blue, N = 69) braid unlinking (± SEM), plotted against force. Assays in A-D were conducted using 0.5 nM topo VI and 1 mM ATP, at 21 °C, over a force range of 0–4 pN.( E) The average rate of relaxation of negative supercoils (events min–1) (± SEM, N tethers across all data points = 12), plotted against force. (F) The average rate of relaxation of positive supercoils (events min–1) (± SEM, N tethers across all data points = 15), plotted against force. Assays in Figures E-F were conducted using 0.75 nM topo VI and 1 mM ATP, at 21 °C.
Figure 6—figure supplement 1—source data 1. Source data is in the file Figure 6—figure supplement 1.