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

  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},
  volume={141 11},
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.



Thermomechanics of DNA: theory of thermal stability under load.

A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B-DNA,

Structural transitions and elasticity from torque measurements on DNA

Tests of the linearity of DNA's twist elasticity, direct measurements of the torsional modulus, characterization of torque-induced structural transitions, and the establishment of a framework for future assays of torque and twist generation by DNA-dependent enzymes are reported.

Thermal denaturation of fluctuating DNA driven by bending entropy.

A statistical model of homopolymer DNA, coupling internal base-pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques, leading, e.g., to a coherent explanation for the experimentally observed thermal viscosity transition.

Temperature-Dependent Signatures of Coherent Vibrational Openings in DNA

We report numerical simulations of the contribution of the transverse hydrogen bond stretching vibrations in the dynamic structure factor of a DNA sequence. We apply a simple nonlinear dynamical

DNA overwinds when stretched

It is shown that for small distortions, contrary to intuition, DNA overwinds under tension, reaching a maximum twist at a tension of ∼30 pN, and the observed twist–stretch coupling predicts that DNA should also lengthen when overwound under constant tension, an effect that is quantitatively confirmed.

Structural transitions in DNA driven by external force and torque.

A simple statistical-mechanical model can be used to globally fit experimental force-extension data of Léger et al. over a wide range of DNA molecule twisting, obtaining the mean twists, extensions, and free energies of the five DNA states found experimentally.

Structural Transitions of a Twisted and Stretched DNA Molecule

Results of a micromanipulation study of single double-helical DNA molecules at forces up to 150 pN are reported, finding that four DNA states are needed to describe the experiments.

Elastic rod model of a supercoiled DNA molecule

The extension fluctuations of a stretched and supercoiled DNA molecule, both at fixed torque and at fixed supercoiling angle, are studied, and the theoretical predictions are compared to some preliminary experimental data.

Coupling between denaturation and chain conformations in DNA: stretching, bending, torsion and finite size effects.

The authors' discrete helical wormlike chain model takes explicitly into account the three elastic degrees of freedom, namely stretching, bending and torsion of the polymer, and contributes to bubble nucleation (opening of base-pairs), which sheds light on the DNA melting mechanism.

Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength

This work investigates the appearance of DNA instability under specific external applied force and imposed twist values, which was revealed by an increase in the temporal fluctuations in the DNA extension, which is found to be linearly correlated to the melting temperature of the DNA double strands.