Defect-facilitated buckling in supercoiled double-helix DNA

Sumitabha Brahmachari, Andrew Dittmore, Yasuharu Takagi, Keir C. Neuman, and John F. Marko
Phys. Rev. E 97, 022416 – Published 28 February 2018

Abstract

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 the coexistence of multiple plectoneme domains in long DNA molecules at physiological salt concentrations (0.1M Na+) and stretching forces (1pN). We find a 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 [A. Dittmore et al., Phys. Rev. Lett. 119, 147801 (2017)] 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 the coexistence of three states at the buckling and rebuckling transitions, which warrants new experiments.

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  • Received 1 December 2017
  • Revised 2 February 2018

DOI:https://doi.org/10.1103/PhysRevE.97.022416

©2018 American Physical Society

Physics Subject Headings (PhySH)

Physics of Living SystemsStatistical Physics & Thermodynamics

Authors & Affiliations

Sumitabha Brahmachari1, Andrew Dittmore2, Yasuharu Takagi2, Keir C. Neuman2, and John F. Marko1,3

  • 1Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
  • 2Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
  • 3Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA

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Issue

Vol. 97, Iss. 2 — February 2018

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