FIG. 3.

The four parameters describing the CS, as a function of applied force. The circles represent values calculated from experimental data taken at two different overall DNA lengths L. The coexisting torque τ and the slope of extension versus linking number q describe the coexistence of the plectoneme helix and the stretched phase. The values ℱ₀ and x₀ describe the extra free energy and extension necessary to form the end loop and tails of the plectoneme. All four values should be independent of length—we suspect the discrepancy in x₀ between the two measured lengths could be due to sequence-dependence. Model predictions for our simulation and Marko’s model [3] are shown as solid and dashed lines, respectively. The simple end-loop model uses average τ and q values from the experiment to predict ℱ₀ and x₀, shown as dot-dashed lines.