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

Wang, Yongzhao; Zhang, Qichang; Wang, Wei

doi:10.1007/s10867-014-9345-0

Cited by 2 publications

(4 citation statements)

References 12 publications

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“…where f i refers to the interfacial traction, which characterizes the effects of the intracellular solution on the rod (Xiao et al, 2014;Wang et al, 2014).…”

Section: Kirchhoff's Equationsmentioning

confidence: 99%

“…The interaction between the DNA elastic rod and the molecules of the solution plays a significant role in the reconfiguration of the DNA segments (Benham and Mielke, 2005). Several studies (Huang, 2011;Xiao et al, 2014;Wang et al, 2014) have shown that microequilibrium configurations of DNA chains are affected by the interaction of the DNA molecule with positive ions in a salt solution. Huang (2011) modeled the interaction using distributed traction, which is caused due to interfacial energy, in a Kirchhoff model, and characterized the folding and unfolding of DNA chains using a numerical simulation of the elastic model.…”

Section: Introductionmentioning

confidence: 99%

“…Huang (2011) modeled the interaction using distributed traction, which is caused due to interfacial energy, in a Kirchhoff model, and characterized the folding and unfolding of DNA chains using a numerical simulation of the elastic model. However, Huang had incorrectly determined the interfacial traction on the central axis of the DNA elastic rod, which was later corrected by two different groups of researchers (Xiao et al, 2014;Wang et al, 2014) in 2014. This interaction should, in essence, be characterized by van der Waals forces or electrostatic forces and is a very critical factor in studying DNA reconfiguration.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of DNA equilibrium configuration under interfacial traction

Qc²,

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Kirchhoff thin elastic rod models are important in the study of the mechanism determining the configurations of flexible structures not only at the macroscopic but also at the microscopic scale. In this study, the energy balance method has been well applied to analyze the configuration of a DNA elastic rod in the presence of interfacial traction. An approximate solution for the shape equations has been obtained, and the relationship between the interfacial factor and the configuration of the DNA segment is derived. The results may provide an explanation for the onset of the formation of kinks in DNA when immersed in a solution.

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“…where f i refers to the interfacial traction, which characterizes the effects of the intracellular solution on the rod (Xiao et al, 2014;Wang et al, 2014).…”

Section: Kirchhoff's Equationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Analysis of DNA equilibrium configuration under interfacial traction

Qc²,

et al. 2016

Genet. Mol. Res.

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“…In salt solution, the geometrical configuration of a DNA chain is determined by the interaction between DNA chain and solution molecules. Huang [9] modeled the interaction by the interfacial traction in an elastic rod model, which characterized DNA folding and unfolding, and Wang et al [10] corrected the incorrect tractions induced by the interfacial energy. Xiao et al [11] used the elastic rod model to evaluate the effects of ionic concentration on the equilibrium configuration.…”

mentioning

confidence: 99%

Helical configurations of elastic rods in the presence of interfacial traction

Wang

Zhang

Wang

et al. 2015

Trans. Tianjin Univ.

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Abstract：The Kirchhoff thin elastic rod models are always the important basis to explore the configuration mechanism of the flexible structures in both the macroscopic and microscopic scale. As a continuum model of DNA, a thin elastic rod subjected to interfacial interactions is used to investigate the helical equilibrium configuration of DNA in salt solution. In this paper, the Kirchhoff's equations in the presence of interfacial traction and the free energy density functions of different configurations are studied. The transition formula of the free energy between B-DNA and Z-DNA is obtained, and the results show that the free energy of the transition is mainly determined by the salt concentration, which agrees well with the experimental data.The genetic information in living cells is carried in the linear sequence of nucleotides in DNA(deoxyribonucleic acid), and it is a double helix in which two polynucleotide chains wind right-or left-handedly around a common central axis. It is generally believed that the elastic properties of DNA are very important in determining its higher-order structures and biological functions [1] . For example, during the processes of replication and transcription of DNA, the structures of topological properties of molecular chains play a significant role in the translation of messenger RNA (ribonucleic acid), and the binding and dissociation of proteins [2] . Characterizing the elastic properties of DNA molecules is of crucial importance in understanding its biological functions. In recent years, the geometrical configuration of the DNA chain has attracted considerable attention. The analytical models based on classical elasticity theory [3][4][5] have no spatial/temporal limitations and have been widely used to study the DNA configuration.DNA deformation, which has important biological functions, is mostly due to the interaction between DNA chain and the environment. For instance, protein operation [6] , temperature change [7] , as well as ion concentration can all induce DNA deformation. DNA under physiological conditions is always in an intracellular solution. The interaction of the DNA chain with the intracellular solution(DNA-solution interaction)is a very important determinant of the DNA configuration [8] . In salt solution, the geometrical configuration of a DNA chain is determined by the interaction between DNA chain and solution molecules. Huang [9] modeled the interaction by the interfacial traction in an elastic rod model, which characterized DNA folding and unfolding, and Wang et al [10] corrected the incorrect tractions induced by the interfacial energy. Xiao et al [11] used the elastic rod model to evaluate the effects of ionic concentration on the equilibrium configuration.Modeling helices in various practical problems has attracted research interest of scientists from widespread areas, including physicists, chemists, applied mathematicians, engineers and biologists. The helices modeled included the morphologies of calcites and silica-barium carbonate ropes, polyeth...

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

Cited by 2 publications

References 12 publications

Analysis of DNA equilibrium configuration under interfacial traction

Analysis of DNA equilibrium configuration under interfacial traction

Helical configurations of elastic rods in the presence of interfacial traction

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