RT Journal Article SR Electronic T1 Defect-Facilitated Buckling in Supercoiled Double-Helix DNA JF bioRxiv FD Cold Spring Harbor Laboratory SP 259689 DO 10.1101/259689 A1 Sumitabha Brahmachari A1 Andrew Dittmore A1 Yasuharu Takagi A1 Keir C. Neuman A1 John F. Marko YR 2018 UL http://biorxiv.org/content/early/2018/02/04/259689.abstract AB We present a statistical-mechanical model for stretched twisted double-helix DNA, where thermal fluctuations are treated explicitly from a Hamiltonian without using any scaling hypotheses. Our model applied to defect-free supercoiled DNA describes coexistence of multiple plectoneme domains in long DNA molecules at physiological salt concentrations (≈ 0.1 M Na+) and stretching forces (≈ 1 pN). We find higher (lower) number of domains at lower (higher) ionic strengths and stretching forces, in accord with experimental observations. We use our model to study the effect of an immobile point defect 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 bending energy of the defect-facilitated kinked end loop. We find that a defect can spatially pin a plectoneme domain via nucleation of a kinked end loop, in accord with experiments and simulations. Our model explains previously-reported magnetic tweezer experiments [1] showing two buckling signatures: buckling and ‘rebuckling’ in supercoiled DNA with a base-unpaired region. Comparing with experiments, we find that under 1 pN force, a kinked end loop nucleated at a base-mismatched site reduces the bending energy by ≈ 0.7 kBT per unpaired base. Our model predicts coexistence of three states at the buckling and rebuckling transitions that warrants new experiments.