DNA mechanics.

  title={DNA mechanics.},
  author={Craig J. Benham and S. P. Mielke},
  journal={Annual review of biomedical engineering},
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… 

Figures from this paper

Kinetic Pathway of Torsional DNA Buckling.
It is found that the decrease in entropy from pinning roughly balances the increase in bending energy, explaining why defects have little effect on buckling rates.
Torsional behaviour of supercoiled DNA regulates recognition of architectural protein Fis on minicircle DNA
It is found that DNA supercoiling favours formation of juxtaposition sites where proteins can perform intersegmental transfer between the spatially close sites and variation in protein diffusivity on different supercoiled DNA also influences the shape of the latter.
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 and represents a ubiquitous motif in higher-order DNA structures and is known to be implicated in the genetic functions.
Nucleosome dynamics: Sequence matters.
DNA-Directed Base Pair Opening
Observations suggest a new molecular mechanism for the initial steps of strand separation in which the coupling of the DNA tertiary and secondary interactions both actively triggers the base pair opening and stabilizes the intermediate states during the melting pathway.
How topological constraints facilitate growth and stability of bubbles in DNA.
An elastic model incorporating topological constraint is shown that, when a stretched double helix is underwound above a critical value of twist, a bubble can spontaneously form, yielding extension and torque behaviors quantitatively in agreement with magnetic tweezers experiments.
Comment on “Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding”
With the use of the correct tractions, new numerical results are presented, which for the values given by Zaixing Huang do not give rise to the physical behavior observed for DNA by the author.
Electrostatic bending response of a charged helix.
This work analyzes how the energy difference ΔE between the bent and the unbent helical chain scales with the length of the helical segment and the radius of curvature and identifies features that are not captured by the standard notion of the bending rigidity.


Conformational and thermodynamic properties of supercoiled DNA.
Solvent effects on supercoiled DNA dynamics explored by Langevin dynamics simulations.
  • Ramachandran, Schlick
  • Physics
    Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
  • 1995
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.
Macroscopic modeling and simulations of supercoiled DNA with bound proteins
General methods are presented for modeling and simulating DNA molecules with bound proteins on the macromolecular level, based on the wormlike chain model of long DNA molecules, which account for basic elements of protein binding effects on DNA local structure but remain computational tractable.
Kinetics of DNA supercoiling studied by Brownian dynamics simulation
We have developed a model for the simulation of the structure and dynamics of covalently closed circular DNA. It is based on the generalization of the original Brownian dynamics algorithm [D. L.
Trefoil Knotting Revealed by Molecular Dynamics Simulations of Supercoiled DNA
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.
Elastic stability of DNA configurations. I. General theory.
Criteria enabling one to determine whether a calculated equilibrium configuration of a DNA segment is stable in the sense that it gives a local minimum to the sum of the segment's elastic energy and the potential of forces acting on it are presented.
Computer simulation of DNA supercoiling.
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.
Finite element analysis of DNA supercoiling
A DNA polymer with hundreds or thousands of base pairs is modeled as a thin elastic rod. To find the equilibrium configurations and associated elastic energies as a function of linking number