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Defect-Facilitated Buckling in Supercoiled Double-Helix DNA

Sumitabha Brahmachari, Andrew Dittmore, Yasuharu Takagi, Keir C. Neuman, John F. Marko
doi: https://doi.org/10.1101/259689
Sumitabha Brahmachari
1Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
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Andrew Dittmore
2Laboratory of Single Molecule Biophysics, National Heart, Lung,and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Yasuharu Takagi
2Laboratory of Single Molecule Biophysics, National Heart, Lung,and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Keir C. Neuman
2Laboratory of Single Molecule Biophysics, National Heart, Lung,and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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John F. Marko
1Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
3Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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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 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 04, 2018.
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Defect-Facilitated Buckling in Supercoiled Double-Helix DNA
Sumitabha Brahmachari, Andrew Dittmore, Yasuharu Takagi, Keir C. Neuman, John F. Marko
bioRxiv 259689; doi: https://doi.org/10.1101/259689
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Defect-Facilitated Buckling in Supercoiled Double-Helix DNA
Sumitabha Brahmachari, Andrew Dittmore, Yasuharu Takagi, Keir C. Neuman, John F. Marko
bioRxiv 259689; doi: https://doi.org/10.1101/259689

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