Defect-Facilitated Buckling in Supercoiled DNA

We present a statistical-mechanical model for double-helix DNA with a defect, where the defect is characterized by an immobile point on the DNA contour that allows a localized kink. The degree of the kink is controlled by the defect size, such that a larger defect further reduces the energy of a defect-facilitated DNA kink. We find that defects can spatially trap a plectoneme domain via nucleation of a kinked end loop. Our model explains previously-reported magnetic tweezer experiments showing two buckling signatures in supercoiled DNA containing a base-unpaired region [Dittmore et al, Phys. Rev. Lett. (2017)]. Our model also predicts coexistence of multiple states at the second buckling or 'rebuckling' point, which warrants new experimental investigations.