FIG. 7.

Buckling transition for various defect sizes. (a) Schematic of the three possible states at the buckling transition: unbuckled state (℘₀₀, blue dashed line), defect-pinned plectoneme (℘₁₀, green solid line), and mobile plectoneme domain (℘₀₁, red dot-dashed line). (b) Total probability of the three states at the buckling transition (ΔLk=19.5 under f = 2 pN and 0.5 M Na⁺, see Fig. 6) as a function of the defect size ε. For larger defects (ε > 0.1), the defect-pinned domain (℘₁₀) is the favored post-buckling state, because of the lower bending energy of a kinked end loop associated with ℘₁₀. While, for small defects (ε < 0.1) the bending energy saved from a kinked end loop is lower than the loss of diffusion entropy of the pinned state (℘₁₀), which makes the mobile domain (℘₀₁) the favored post-buckling state. Note the relatively higher probability of the unbuckled state for smaller defects. This is due to a shift of the buckling point towards lower linking numbers with increasing defect sizes (Fig. 10). (c) Probability density of DNA extension at the buckling transition shows the typical bimodal character observed for defect-free DNA (Fig. 2), however, the defect size controls the states populating the lower-extension mode of the distribution. This also suggests that measurement of the extension alone is insufficient to distinguish between the states involved at the buckling transition.