Fig. 1.

a Representative structures from an atomistic molecular dynamics (MD) simulation of a 108-bp negatively supercoiled DNA minicircle (σ ≈ −0.1): left untwisted planar circular conformation, middle negatively writhed (Wr) conformation, right relief of superhelical stress by defect formation (Defect; in red). b Representative structures from an atomistic MD simulation of a 336-bp negatively supercoiled DNA minicircle (σ ≈ −0.1): left untwisted planar circular conformation, middle negatively writhed (Wr) conformation, right partial superhelical stress relaxation due to defect formation (Defect; in red). Minus signs indicate the degree of untwisting or writhing (e.g. Twist - - - indicates that the circle is underwound by three turns)