Figure 1.

Arising supercoiling pushes trefoil knot out of the linear DNA. Snapshots from one continuous molecular dynamics simulation (see methods) where gyrase starts introducing negative supercoiling into knotted linear DNA that is ca 3 kb long. The site of active swivel (gyrase) is shown as the blue bead. (A) Starting configuration of knotted linear DNA molecule. (B) Formation of plectonemes starts in the vicinity of active gyrase. (C, D). As plectonemically wound region increases it effectively pushes DNA segments that intervene with formation of relatively regular interwound regions. This process induces slithering of the knotted portion of the molecule towards the ends of knotted linear DNA and leads to its unknotting.