Conformation transitions of a polyelectrolyte chain: A replica-exchange Monte-Carlo study

Chi, Peng; Li, Baohui; Shi, An‐Chang

doi:10.1103/physreve.84.021804

Cited by 11 publications

(6 citation statements)

References 21 publications

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“…We set α = 0.5 and β = 2 to ensure that the two linear chains in a ds-oligo molecule form a ladder. The long-range Coulomb interactions are described in the same form as we used before. , That is, U el = (∑ i < j q i q j /( Dr i,j )), where q i,j = ± e , D is the dielectric constant of the medium, r i,j is the distance between two charges, and with the summation extending over all charges. The long-range interactions are computed using an approximation of the Ewald summation.…”

Section: Methodsmentioning

confidence: 99%

Effect of Peptide Charge Distribution on the Structure and Kinetics of DNA Complex

Zhao

Zhu

et al. 2015

Macromolecules

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The complexes formed by DNA or siRNA interacting with polycations showed great potential as nonviral vectors for gene delivery. The physicochemical properties of the DNA/siRNA complexes, which could be tuned by adjusting the characteristics of polycations, were directly related to their performance in gene delivery. Using 21 bp double-stranded oligonucleotide (ds-oligo) and two icosapeptides (with the repeating units being KKGG and KGKG, respectively) of the same charge density as model molecules, we investigated the effect of charge distribution on the kinetics of complexation and the structure of the final complexes. Even though the distribution of the charged groups in peptides was only adjusted by one position, the complexes formed by (KKGG) 5 and ds-oligo were larger in size and easier to precipitate than those formed by (KGKG) 5 . Counterintuitively, it was not the charged groups but the hydrophilic neutral spacers that determined the kinetics and the structure of the complex. We attributed such an effect to the water-mediated disproportionation process. The hydrophilic spacers next to each other were better than that in the separated pattern in holding water molecules after forming the complex. The water-rich domains in the complex functioned as a lubricant and facilitated the relaxation of the polyelectrolyte, resulting in a fast complexation process. The resulting complex was thus larger in size and lower in surface energy.

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Section: Methodsmentioning

confidence: 99%

Effect of Peptide Charge Distribution on the Structure and Kinetics of DNA Complex

Zhao

Zhu

et al. 2015

Macromolecules

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“…A weak‐adsorption limit is investigated for weakly charged PEs, below the Manning counterion condensation threshold,64, 65 with no counterion‐mediated attraction66, 67 between the PE segments. The linear PE charge density is $\rho = e_0 /b_0$ , where e 0 is the elementary charge and b 0 is the PE intercharge separation.…”

Section: Modeling Pe Adsorptionmentioning

confidence: 99%

Critical polyelectrolyte adsorption under confinement: Planar slit, cylindrical pore, and spherical cavity

Cherstvy

2012

Biopolymers

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We explore the properties of adsorption of flexible polyelectrolyte chains in confined spaces between the oppositely charged surfaces in three basic geometries. A method of approximate uniformly valid solutions for the Green function equation for the eigenfunctions of polymer density distributions is developed to rationalize the critical adsorption conditions. The same approach was implemented in our recent study for the "inverse" problem of polyelectrolyte adsorption onto a planar surface, and on the outer surface of rod-like and spherical obstacles. For the three adsorption geometries investigated, the theory yields simple scaling relations for the minimal surface charge density that triggers the chain adsorption, as a function of the Debye screening length and surface curvature. The encapsulation of polyelectrolytes is governed by interplay of the electrostatic attraction energy toward the adsorbing surface and entropic repulsion of the chain squeezed into a thin slit or small cavities. Under the conditions of surface-mediated confinement, substantially larger polymer linear charge densities are required to adsorb a polyelectrolyte inside a charged spherical cavity, relative to a cylindrical pore and to a planar slit (at the same interfacial surface charge density). Possible biological implications are discussed briefly in the end.

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“…Parallel to the development of theories, computer simulations have been employed to the study of polyelectrolyte systems, which greatly enhanced our qualitative understanding of nucleic acid–ion interaction, since ss nucleic acid is a special one of polyelectrolytes and shares some general ion‐dependent properties. However, until now, the simulational investigations were either based on different‐level approximations or ignored specific nucleic acid structural features . For example, most of them investigated macroscopic properties of bead‐spring model of polyelectrolytes in salt‐free or explicit dilute salt solutions, or predicted DNA structure changes by accounting for ion effects through a screened DH potential .…”

Section: Introductionmentioning

confidence: 99%

“…However, until now, the simulational investigations were either based on different-level approximations or ignored specific nucleic acid structural features. [37][38][39][40][41][42][43] For example, most of them investigated macroscopic properties of bead-spring model of polyelectrolytes in salt-free or explicit dilute salt solutions, or predicted DNA structure changes by accounting for ion effects through a screened DH potential. [37][38][39][40][41][42][43] Beyond the coarse-grained simulation models, all-atom simulations can capture the molecule structures and solvent details at atomistic level.…”

Section: Introductionmentioning

confidence: 99%

“…[37][38][39][40][41][42][43] For example, most of them investigated macroscopic properties of bead-spring model of polyelectrolytes in salt-free or explicit dilute salt solutions, or predicted DNA structure changes by accounting for ion effects through a screened DH potential. [37][38][39][40][41][42][43] Beyond the coarse-grained simulation models, all-atom simulations can capture the molecule structures and solvent details at atomistic level. [44][45][46][47] But for ss chain with strong conformational fluctuation, all-atom simulations are computationally too expensive.…”

Section: Introductionmentioning

confidence: 99%

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Salt contribution to the flexibility of single‐stranded nucleic acid of finite length

Wang

Tan

2013

Biopolymers

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Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this paper, the salt effects on the flexibility of single-stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse-grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual-bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and trivalent/small divalent ions can both induce more compact state than a random relaxation state. We found that monovalent, divalent and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion-exclusion-volume effect to ion Coulomb correlations. In addition, the predicted Na + and Mg 2+-dependent persistence length l p 's of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for l p as a function of [Na + ], [Mg 2+ ] and chain length.

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Conformation transitions of a polyelectrolyte chain: A replica-exchange Monte-Carlo study

Cited by 11 publications

References 21 publications

Effect of Peptide Charge Distribution on the Structure and Kinetics of DNA Complex

Effect of Peptide Charge Distribution on the Structure and Kinetics of DNA Complex

Critical polyelectrolyte adsorption under confinement: Planar slit, cylindrical pore, and spherical cavity

Salt contribution to the flexibility of single‐stranded nucleic acid of finite length

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