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…
46 Citations
Kinetic Pathway of Torsional DNA Buckling.
- EngineeringThe journal of physical chemistry. B
- 2018
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
- BiologyNucleic Acids Research
- 2022
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
- Biology
- 2012
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.
Determining DNA supercoiling enthalpy by isothermal titration calorimetry.
- ChemistryBiochimie
- 2012
DNA-Directed Base Pair Opening
- BiologyMolecules
- 2012
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.
- PhysicsBiophysical journal
- 2008
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”
- Biology, PhysicsJournal of biological physics
- 2014
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.
- PhysicsPhysical review. E
- 2018
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.
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