Figure 3.

Partitioning of supercoiling. (A) A completely relaxed plasmid molecule. There are 12 turns of the double helix, and, as the helix does not cross over itself, the twist (Tw) is equal to 12 and writhe (Wr) is equal to 0. (B) The same plasmid molecule as in a), but supercoiled. The double helix has been untwisted by 2 turns but does not cross over itself, leading to Tw = 10 and Wr = 0. ( C) The supercoiled molecule in b can release some of the undertwisting stress energy by crossing the double helix over itself. Here, Tw = 12 while Wr = −2. (D) Another means of relieving stress energy is through site unwinding, depicted here for the same plasmid as in B and C. Whether a plasmid partitions its energy into Tw, Wr, or other secondary structures, such as unwinding, is probabilistic for each base pair, and depends on its local energy landscape.