Nucleation at the DNA supercoiling transition.

  title={Nucleation at the DNA supercoiling transition.},
  author={B. Daniels and J. Sethna},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  volume={83 4 Pt 1},
  • B. Daniels, J. Sethna
  • Published 2011
  • Chemistry, Medicine, Materials Science, Physics, Biology
  • Physical review. E, Statistical, nonlinear, and soft matter physics
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition-state theory, we predict the rate of this plectoneme nucleation to be of order 10(4) Hz. We reconcile this with experiments that have measured hopping rates of order 10 Hz by noting that the viscous drag on the bead used to manipulate the DNA limits the measured rate. We find that the intrinsic bending caused by disorder in the… Expand
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Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
A novel conformational regime for DNA is predicted, where denaturation bubbles form at the tips of plectonemes, and its properties are studied using coarse-grained simulations for negative supercoiling. Expand
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The authors' discrete wormlike chain model is employed to bypass experimental limitations and simulate the dynamic response of supercoiled DNA to a single strand nick and makes three major observations. Expand
Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices
In magnetic tweezers experiments, torsionally-stressed stretched braids supercoil via an abrupt buckling transition, which is associated with nucleation of a braid end loop, and that the buckled braid is characterized by proliferation of multiple domains. Expand
Torque and buckling in stretched intertwined double-helix DNAs.
A statistical-mechanical model for the behavior of intertwined DNAs is presented, with a focus on their torque and extension as a function of their catenation (linking) number and applied force, and it is found that buckling occurs near the point where experiments have observed a kink in the extension versus linking number. Expand
Coarse-grained modelling of supercoiled RNA.
OxRNA, a recently developed coarse-grained model of RNA, exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations, and predicts denaturation bubble formation in plectoneme end-loops, suggesting preferential plect oneme localisation in weak base sequences. Expand
Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA.
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  • 2012
A detailed mesoscopic model is presented for the formation of plectonemic domains, including their positional entropy, and the influence of small chiral loops or "curls" along the extended DNA, and it is shown how addition of loop-trapping enzymes can modify the supercoiling transition. Expand
Statistical mechanics of nucleic acids under mechanical stress
In this thesis, the response of DNA and RNA to linear and torsional mechanical stress is studied using coarse-grained models. Inspired by single-molecule assays developed over the last two decades,Expand


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  • Medicine
  • Protein science : a publication of the Protein Society
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  • Rev. Lett. 100, 148301
  • 2008
  • Rev. E 55, 7364
  • 1997
  • 254, 579
  • 1995
  • Mod. Phys. 62, 251
  • 1990
  • J. 98, 1267
  • 2010
Biophys . J
  • Biophys . J
  • 2010