DNA denaturation bubbles: free-energy landscape and nucleation/closure rates.

@article{Sicard2015DNADB,
  title={DNA denaturation bubbles: free-energy landscape and nucleation/closure rates.},
  author={François Sicard and Nicolas Destainville and Manoel Manghi},
  journal={The Journal of chemical physics},
  year={2015},
  volume={142 3},
  pages={
          034903
        }
}
The issue of the nucleation and slow closure mechanisms of non-superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (respectively, closure) of an approximately 10 base-pair bubble, in agreement with… 
Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles.
We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of
Direct observation of breathing dynamics at the mismatch induced DNA bubble with nanometre accuracy: a smFRET study.
The detailed conformational dynamics of the melted region in double-stranded DNA has been studied using a combination of ensemble and single-molecule FRET techniques. We monitored the millisecond
Physics of base-pairing dynamics in DNA
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both
Double-stranded coarse grained model for DNA: applications to supercoiling and denaturation
DNA supercoiling is the name given to the under or overwinding of the two strands of a DNA double helix. It is of great interest because it is relevant in several crucial biological processes.
Probing the mechanical properties of DNA nanostructures with metadynamics
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased
Kinetic theory for DNA melting with vibrational entropy.
TLDR
This work identifies a key bending mode with GHz frequency that replaces the hydrogen vibration modes as the dominant out-of-phase phonon vibration at the transition state and associates its bending modulus to a universal in-phase bending vibration modulus at equilibrium.
Elasticity of a DNA chain dotted with bubbles under force.
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles, respectively, when the strands of the
A single nucleotide resolution model for large-scale simulations of double stranded DNA.
TLDR
A mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules for time-scales which are relevant to physiological processes is presented.
Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations.
TLDR
Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.
Mechanics and nanovoid nucleation dynamics: effects of polar functionality in glassy polymer networks.
TLDR
The results suggest that pDCPD tolerates the addition of some polar chemistry without degrading its excellent mechanical properties, and is compatible with networks of similar composition.
...
1
2
3
4
...

References

SHOWING 1-10 OF 92 REFERENCES
Slow closure of denaturation bubbles in DNA: twist matters.
TLDR
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations, yielding a good quantitative agreement with the experiments.
Strand diffusion-limited closure of denaturation bubbles in DNA
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible
A semiflexible chain model of local denaturation in double-stranded DNA.
TLDR
The results show that the entropy associated with semiflexibility of DNA sensitively affects the size distribution and lifetime of bubble, and the lifetime grows with bubble size m as m(2.7) at temperature close to T(c), which is consistent with the analysis based on a stochastic model of bubble size dynamics.
The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA.
TLDR
The results differ considerably from expectations based solely upon considerations of chain configuration in vacuo, indicating the importance of solvent-dependent factors in determining the structure of closed circular DNA.
Torsional stress and local denaturation in supercoiled DNA.
  • C. Benham
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1979
TLDR
It is shown that local denaturation can be a natural consequence of supercoiling, even in environments where base pairing of linear DNA is energetically favored, and that control of local melting by DNA topoisomerases and DNA gyrases could regulate diverse events involved in transcription, replication, recombination, and repair.
Coupling between denaturation and chain conformations in DNA: stretching, bending, torsion and finite size effects.
TLDR
A statistical model coupling denaturation and chain conformations in DNA is developed and the role of an additional loop entropy is explored, which contributes to bubble nucleation (opening of base-pairs), which sheds light on the DNA melting mechanism.
Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA.
TLDR
A model for simulating sequence-dependent DNA strand separation under the nonequilibrium conditions imposed by the dynamic introduction of torsional stress is introduced and it is found that sites susceptible to denaturation show a propensity for localizing to supercoil apices, suggesting that base sequence determines locations of strand separation not only through the energetics of interstrand interactions, but also by influencing the geometry of supercoiling.
Supercoiling induces denaturation bubbles in circular DNA.
TLDR
It is shown that in vivo sustained DNA bubbles are likely to occur due to partial twist release in regions rich in weaker AT base pairs, and an analytical derivation of the probability distribution to find multiple bubbles is derived.
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
TLDR
The structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers are explored, resulting in an "average base" description of DNA.
DNA bubble dynamics as a quantum Coulomb problem.
TLDR
This work studies the dynamics of denaturation bubbles in double-stranded DNA and derives expressions for the bubble survival distribution W(t), demonstrating that the associated Fokker-Planck equation is equivalent to a Coulomb problem.
...
1
2
3
4
5
...