Nucleation at the DNA supercoiling transition.

@article{Daniels2011NucleationAT,
  title={Nucleation at the DNA supercoiling transition.},
  author={B. Daniels and J. Sethna},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  year={2011},
  volume={83 4 Pt 1},
  pages={
          041924
        }
}
  • 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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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
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  • 2012
TLDR
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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References

SHOWING 1-10 OF 53 REFERENCES
Molecular biology and Genomics
TLDR
This book discusses fundamental methods of DNA analysis, as well as suggestions for Career Planning or: The Mini 'Machiavelli' for Young Researchers. Expand
Macromolecules
  • C. Tanford
  • Medicine
  • Protein science : a publication of the Protein Society
  • 1948
TLDR
The formation of a glycosidic linkage is described and the four levels of protein structure are described. Expand
Handbook of Materials Modeling
Handbook of Materials Modeling Volume I Methods and Models Editor Sidney Yip, Massachusetts Institute of Technology Subject Editors Martin Bazant, Massachusetts Institute of Technology BruceExpand
Ann
Aaron Beck’s cognitive therapy model has been used repeatedly to treat depression and anxiety. The case presented here is a 34-year-old female law student with an adjustment disorder with mixedExpand
Phys
  • Rev. Lett. 100, 148301
  • 2008
Phys
  • Rev. E 55, 7364
  • 1997
Biol
  • 254, 579
  • 1995
Rev
  • Mod. Phys. 62, 251
  • 1990
Biophys
  • J. 98, 1267
  • 2010
Biophys . J
  • Biophys . J
  • 2010
...
1
2
3
4
5
...