Torque-induced deformations of charged elastic DNA rods: thin helices, loops, and precursors of DNA supercoiling

Cherstvy, Andrey G.

doi:10.1007/s10867-010-9211-7

Cited by 15 publications

(20 citation statements)

References 46 publications

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“…Benham [2,3] and Le Bret [4,5] firstly used the elastic model to analyze the equilibrium configuration of DNA. In the framework of this model, varied subjects related with the DNA configuration were investigated extensively [6][7][8][9][10]. Some geometrical configurations appearing in the DNA condensation have been explained perfectly.…”

Section: Introductionmentioning

confidence: 99%

“…Some geometrical configurations appearing in the DNA condensation have been explained perfectly. Recently, Cherstvy used the elastic model to further investigate the effect of counterions and attractive inter-segmental DNA-DNA interactions on molecular spatial conformations and the low-dielectric DNA core on the elastic DNA properties [9][10][11] in a micro field. Up to the present, it has been confirmed that the elastic rod model is adequate for characterizing the geometrical configuration and deformation of DNA.…”

Section: Introductionmentioning

confidence: 99%

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An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution

2014

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As a coarse-gained model, a super-thin elastic rod subjected to interfacial interactions is used to investigate the condensation of DNA in a multivalent salt solution. The interfacial traction between the rod and the solution environment is determined in terms of the Young-Laplace equation. Kirchhoff's theory of elastic rod is used to analyze the equilibrium configuration of a DNA chain under the action of the interfacial traction. Two models are established to characterize the change of the interfacial traction and elastic modulus of DNA with the ionic concentration of the salt solution, respectively. The influences of the ionic concentration on the equilibrium configuration of DNA are discussed. The results show that the condensation of DNA is mainly determined by competition between the interfacial energy and elastic strain energy of the DNA itself, and the interfacial traction is one of forces that drive DNA condensation. With the change of concentration, the DNA segments will undergo a series of alteration from the original configuration to the condensed configuration, and the spiral-shape appearing in the condensed configuration of DNA is independent of the original configuration.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution

2014

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“…The other was to generate a better general understanding, as well as a systematic theoretical analysis, of the role of electrostatic interactions in braided DNA pairs, e.g., as a first step toward studying these effects in supercoiled plasmids. Most previous studies of DNA braiding and supercoiling focused on the topology and mechanics of the double helices (17)(18)(19)(20), although some have included electrostatics (21)(22)(23) by treating DNA as a uniformly charged rod. Recent studies suggest that chiral DNA-DNA interactions may actually play a very important role in DNA braiding and plasmid supercoiling (13,24).…”

Section: Introductionmentioning

confidence: 99%

Electrostatic Braiding and Homologous Pairing of DNA Double Helices

Cortini

Kornyshev

Lee

et al. 2011

Biophysical Journal

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Homologous pairing and braiding (supercoiling) have crucial effects on genome organization, maintenance, and evolution. Generally, the pairing and braiding processes are discussed in different contexts, independently of each other. However, analysis of electrostatic interactions between DNA double helices suggests that in some situations these processes may be related. Here we present a theory of DNA braiding that accounts for the elastic energy of DNA double helices as well as for the chiral nature of the discrete helical patterns of DNA charges. This theory shows that DNA braiding may be affected, stabilized, or even driven by chiral electrostatic interactions. For example, electrostatically driven braiding may explain the surprising recent observation of stable pairing of homologous double-stranded DNA in solutions containing only monovalent salt. Electrostatic stabilization of left-handed braids may stand behind the chiral selectivity of type II topoisomerases and positive plasmid supercoiling in hyperthermophilic bacteria and archea.

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“…Finally, it should be noted that, this is only a coarse-grained model characterizing interaction potentials between DNA segments and solution, and the deformations of elastic under applied end forces [2,3,10] should be considered in future models.…”

Section: Discussionmentioning

confidence: 99%

Comment on “Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding”

2014

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In this comment, we point out that the tractions induced by interfacial energy, which are referred to as the tractions on the central axis curve of the DNA elastic rod presented by Huang (J. Biol. Phys. 37(1), 79-90, 2011), are incorrect. The correct tractions are provided in this literature. Further, with the use of the correct tractions, we present new numerical results, which for the values given by Zaixing Huang do not give rise to the physical behavior observed for DNA by the author.

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Torque-induced deformations of charged elastic DNA rods: thin helices, loops, and precursors of DNA supercoiling

Cited by 15 publications

References 46 publications

An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution

An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution

Electrostatic Braiding and Homologous Pairing of DNA Double Helices

Comment on “Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding”

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