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Gordon Southam - One of the best experts on this subject based on the ideXlab platform.

Maggy F Lengke - One of the best experts on this subject based on the ideXlab platform.

Michael E Fleet - One of the best experts on this subject based on the ideXlab platform.

John F. Marko - One of the best experts on this subject based on the ideXlab platform.

  • defect facilitated buckling in supercoiled double helix dna
    Physical Review E, 2018
    Co-Authors: Sumitabha Brahmachari, Andrew Dittmore, Keir C. Neuman, Yasuharu Takagi, John F. Marko
    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)PRLTAO0031-900710.1103/PhysRevLett.119.147801] 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 k_{B}T per unpaired base. Our model predicts the coexistence of three states at the buckling and rebuckling transitions, which warrants new experiments.

  • defect facilitated buckling in supercoiled double helix dna
    Physical Review E, 2018
    Co-Authors: Sumitabha Brahmachari, Andrew Dittmore, Keir C. Neuman, Yasuharu Takagi, John F. Marko
    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 ($\ensuremath{\approx}0.1\phantom{\rule{0.16em}{0ex}}\mathrm{M} {\mathrm{Na}}^{+}$) and stretching forces ($\ensuremath{\approx}1\phantom{\rule{0.16em}{0ex}}\mathrm{pN})$. 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 $\ensuremath{\approx}0.7 {k}_{B}T$ per unpaired base. Our model predicts the coexistence of three states at the buckling and rebuckling transitions, which warrants new experiments.

  • defect facilitated buckling in supercoiled double helix dna
    bioRxiv, 2018
    Co-Authors: Sumitabha Brahmachari, Andrew Dittmore, Keir C. Neuman, Yasuharu Takagi, John F. Marko
    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 showing two buckling signatures: buckling and 9rebuckling9 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 k B T per unpaired base. Our model predicts coexistence of three states at the buckling and rebuckling transitions that warrants new experiments.

  • Supercoiling DNA Locates Mismatches
    Physical Review Letters, 2017
    Co-Authors: Andrew Dittmore, Sumitabha Brahmachari, Yasuhara Takagi, John F. Marko, Keir C. Neuman
    Abstract:

    : We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.6 pN force and show that under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.

Sumitabha Brahmachari - One of the best experts on this subject based on the ideXlab platform.

  • defect facilitated buckling in supercoiled double helix dna
    Physical Review E, 2018
    Co-Authors: Sumitabha Brahmachari, Andrew Dittmore, Keir C. Neuman, Yasuharu Takagi, John F. Marko
    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)PRLTAO0031-900710.1103/PhysRevLett.119.147801] 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 k_{B}T per unpaired base. Our model predicts the coexistence of three states at the buckling and rebuckling transitions, which warrants new experiments.

  • defect facilitated buckling in supercoiled double helix dna
    Physical Review E, 2018
    Co-Authors: Sumitabha Brahmachari, Andrew Dittmore, Keir C. Neuman, Yasuharu Takagi, John F. Marko
    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 ($\ensuremath{\approx}0.1\phantom{\rule{0.16em}{0ex}}\mathrm{M} {\mathrm{Na}}^{+}$) and stretching forces ($\ensuremath{\approx}1\phantom{\rule{0.16em}{0ex}}\mathrm{pN})$. 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 $\ensuremath{\approx}0.7 {k}_{B}T$ per unpaired base. Our model predicts the coexistence of three states at the buckling and rebuckling transitions, which warrants new experiments.

  • defect facilitated buckling in supercoiled double helix dna
    bioRxiv, 2018
    Co-Authors: Sumitabha Brahmachari, Andrew Dittmore, Keir C. Neuman, Yasuharu Takagi, John F. Marko
    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 showing two buckling signatures: buckling and 9rebuckling9 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 k B T per unpaired base. Our model predicts coexistence of three states at the buckling and rebuckling transitions that warrants new experiments.

  • Supercoiling DNA Locates Mismatches
    Physical Review Letters, 2017
    Co-Authors: Andrew Dittmore, Sumitabha Brahmachari, Yasuhara Takagi, John F. Marko, Keir C. Neuman
    Abstract:

    : We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.6 pN force and show that under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.