DNA mechanics.

@article{Benham2005DNAM,
  title={DNA mechanics.},
  author={Craig J. Benham and S. P. Mielke},
  journal={Annual review of biomedical engineering},
  year={2005},
  volume={7},
  pages={
          21-53
        }
}
We review the history of DNA mechanics and its analysis. We evaluate several methods to analyze the structures of superhelical DNA molecules, each predicated on the assumption that DNA can be modeled with reasonable accuracy as an extended, linearly elastic polymer. Three main approaches are considered: mechanical equilibrium methods, which seek to compute minimum energy conformations of topologically constrained molecules; statistical mechanical methods, which seek to compute the Boltzmann… Expand
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37 Citations
Background Citations
16
Methods Citations
1

37 Citations

Citation Type

Citation Type

The Stochastic Elastica and Excluded-Volume Perturbations of DNA Conformational Ensembles.
  • G. Chirikjian
  • Physics, Medicine
  • International journal of non-linear mechanics
  • 2008
TLDR
A coordinate-free Lie-group formulation for generating ensembles of DNA conformations in solution is presented and the accuracy of this approximation is shown to be good when using a numerically generated ensemble of self-avoiding sample paths as the baseline for comparison. Expand
A new approach to the mechanics of DNA: Atoms-to-beam homogenization
Abstract It is useful to describe the deformation characteristics of long biological macromolecules, such as deoxyribonucleic acid (DNA), by means of terms such as “bending”, “stretching”, or… Expand
Lac Repressor Mediated DNA Looping: Monte Carlo Simulation of Constrained DNA Molecules Complemented with Current Experimental Results
TLDR
A new Monte Carlo scheme for accurate simulation of DNA configurations subject to geometric constraints is presented and this method is applied to Lac repressor mediated DNA looping, comparing the simulation results with new experimental data obtained by the TPM technique. Expand
Helical Chirality: a Link between Local Interactions and Global Topology in DNA
TLDR
The present study reveals that the various topological states of the cell are associated with different inter-segmental interactions, which leads to the prediction that, due to their different tertiary intra-molecular interactions, supercoiled molecules of opposite signs must display markedly different physical properties. Expand
Bullied no more: when and how DNA shoves proteins around
TLDR
This work discusses how elastic energy arising from supercoiling and electrostatic energy are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism. Expand
The Mathematics of DNA Sturcture, Mechanics, and Dynamics
A brief review is given of the main concepts, ideas, and results in the fields of DNA topology, elasticity, mechanics and statistical mechanics. Discussion in- cludes the notions of the linking… Expand
A model for structure and thermodynamics of ssDNA and dsDNA near a surface: A coarse grained approach
TLDR
This model parameterized a discretized worm-like chain model to gain insight into longer and surface mounted sequences, and reproduces end to end distance averages from experimental results, in agreement with polymer theory and all atom simulations. Expand
DNA-DNA Recognition: From Tight Contact to Fatal Attraction
The close approach of double helices plays essential roles in the architecture and catalysis of nucleic acids. Transient or long-term DNA-DNA interactions occur in the cell and participate in various… Expand
Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches
TLDR
The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA super coiling and the dynamics of supercoiling in molecular detail. Expand
Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.
TLDR
Under physiologically relevant conditions of lower force and lower salt concentration, plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size, and this framework provides a way to study the effect of defects on DNA super coiling and the dynamics of supercoiling in molecular detail. Expand
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References

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A new large-scale truncated-Newton algorithm for minimization and a Langevin/implicit-Euler scheme for molecular dynamics is applied and the energetic exchange of stability between the circle and the figure-8, in very good agreement with analytical results, is detailed. Expand
Geometry and mechanics of DNA superhelicity
TLDR
This paper analyzes the elastic equilibrium conformations of duplex DNA constrained by the constancy of its molecular linking number, Lk, and compares these toroidal conformations and interwound configurations, which are shown to be stable, although they are not equilibria in the present sense. Expand
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TLDR
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TLDR
Three distinct physical regimes of DNA behavior are identified, characterized by maximal sampling and high mobility of the DNA, and high, random forces, where all of the global modes are effectively frozen by extreme overdamping, offering insight into hydrodynamic effects on supercoiled DNA. Expand
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Kinetics of DNA supercoiling studied by Brownian dynamics simulation
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Trefoil Knotting Revealed by Molecular Dynamics Simulations of Supercoiled DNA
TLDR
A new computational approach is reported that combines an idealized elastic energy model, a compact B-spline representation of circular duplex DNA, and deterministic minimization and molecular dynamics algorithms, and shows the potential effectiveness of the Langevin/ implicit-Euler dynamics scheme for studying biomolecular folding and reactions over biologically interesting time scales. Expand
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TLDR
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