Thermomechanical stability and mechanochemical response of DNA: a minimal mesoscale model.

@article{Nisoli2014ThermomechanicalSA,
  title={Thermomechanical stability and mechanochemical response of DNA: a minimal mesoscale model.},
  author={Cristiano Nisoli and Alan R. Bishop},
  journal={The Journal of chemical physics},
  year={2014},
  volume={141 11},
  pages={
          115101
        }
}
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures for denaturation under torque and stretch, phase diagrams for stable DNA, probe/response profiles under mechanical loads, and the density of dsDNA as a function of stretch and twist. We compare our predictions with available single molecule manipulation… 
3 Citations

Base pair fluctuations in helical models for nucleic acids.

  • M. Zoli
  • Physics
    The Journal of chemical physics
  • 2021
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids, typical of double stranded DNA helices, and the cutoff is found to increase also in the presence of a sliding motion, which shortens the helix contour length.

DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration.

A mesoscopic model calculation based on available experimental data where the terminal base pairs of a DNA duplex are considered separately, showing an important reduction of hydrogen bond strength for terminal cytosine-guanine (CG) base pairs which is uniform over the whole range of salt concentrations, while for AT base pairs, the authors obtain a nearly 1/3 reduction but only at low salt concentrations.

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