Complexation between weakly basic dendrimers and linear polyelectrolytes: effects of grafts, chain stiffness, and pOH

Lewis, Thomas; Pandav, Gunja; Omar, Ahmad K.; Ganesan, Venkat

doi:10.1039/c3sm00062a

Cited by 9 publications

(16 citation statements)

References 60 publications

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“…Whence, we only present the salient modifications to our earlier model to capture the physics of the system considered here. With respect to the framework outlined in ref , the following two additional free energy contributions arise for the model considered in the present article: The translational mixing entropies of the co- and counterions: − β scriptF m i x = prefix∫ normald boldr .25em ∑ k { ρ k false( boldr false) false[ ln nobreak0em.25em⁡ ρ k ( r ) − 1 + β μ k o false] } where ρ k ( r ) ( k = +,−) denotes the local density of the co- and counterions, μ k o represents the chemical potential of the k th species, and β = ( k B T ) −1 where k B denotes the Boltzmann constant. The free energy arising from electrostatic interactions: β scriptF e l e c = prefix∫ normald boldr .25em [ ρ e false( boldr false) Φ false( boldr false) + ε 8 π e 2 | ∇ Φ | 2 ] …”

Section: Theoretical Frameworkmentioning

confidence: 99%

“…The translational mixing entropies of the co- and counterions: − β scriptF m i x = prefix∫ normald boldr .25em ∑ k { ρ k false( boldr false) false[ ln nobreak0em.25em⁡ ρ k ( r ) − 1 + β μ k o false] } where ρ k ( r ) ( k = +,−) denotes the local density of the co- and counterions, μ k o represents the chemical potential of the k th species, and β = ( k B T ) −1 where k B denotes the Boltzmann constant.…”

Section: Theoretical Frameworkmentioning

confidence: 99%

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Interplay between Depletion and Electrostatic Interactions in Polyelectrolyte–Nanoparticle Systems

Pryamitsyn

Ganesan

2014

Macromolecules

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We use a numerical implementation of polymer self-consistent field theory to study the effective interactions between two spherical particles in polyelectrolyte solutions. We consider a model in which the particles possess fixed charge density and the polymers contain a prespecified amount of dissociated charges. We quantify the polymer-mediated interactions between the particles as a function of the particle charge, polymer concentrations and particle sizes. We study the interplay between depletion interactions, which arise as a consequence of polymer exclusion from the particle interiors, and the electrostatic forces which result from the presence of charges on the polymers and particles. Our results indicate that for weakly charged and uncharged particles, the polymer-mediated interactions predominantly consist of a short-range attraction and a long-range repulsion. When the particle charge is increased, the interactions become purely repulsive. A longer range, albeit weaker, bridging attraction was also evident for some parametric regimes. We demonstrate that the short-range attraction and the longer-range repulsion can be modeled as a sum of a depletion-like attraction and an electrostatic Debye–Huckel like repulsion. However, the amplitude and range underlying the depletion and electrostatic interactions are shown to possess a complex relationship to the parameters of our system. We present scaling arguments and analytical theory to rationalize some of the dependencies underlying the parameters governing the interaction potentials.

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Section: Theoretical Frameworkmentioning

confidence: 99%

Section: Theoretical Frameworkmentioning

confidence: 99%

Interplay between Depletion and Electrostatic Interactions in Polyelectrolyte–Nanoparticle Systems

Pryamitsyn

Ganesan

2014

Macromolecules

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“…Aptamers are polyelectrolytic in nature with their monomer units (nucleobases) participating in acid-base equilibrium and counterion binding reactions with the surrounding solution environments. Charge regulation and counterion binding in aptamers, or polyelectrolytes in general, are modulated by the metal ions present in the system, which can non-trivially alter their chemical and structural properties [8,9,10,11,12,13]. The presence of metal ions affects the performance of the aptamers as biosensing probes or therapeutics [14,15,16] due to the electrostatic screening of the charges on their surface, which changes their structure and chemistry.…”

Section: Introductionmentioning

confidence: 99%

Quantifying Mg2+ Binding to ssDNA Oligomers: A Self-Consistent Field Theory Study at Varying Ionic Strengths and Grafting Densities

Jahan

Uline

2018

Polymers

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The performance of aptamer-based biosensors is crucially impacted by their interactions with physiological metal ions, which can alter their structures and chemical properties. Therefore, elucidating the nature of these interactions carries the utmost importance in the robust design of highly efficient biosensors. We investigated Mg 2 + binding to varying sequences of polymers to capture the effects of ionic strength and grafting density on ion binding and molecular reorganization of the polymer layer. The polymers are modeled as ssDNA aptamers using a self-consistent field theory, which accounts for non-covalent ion binding by integrating experimentally-derived binding constants. Our model captures the typical polyelectrolyte behavior of chain collapse with increased ionic strength for the ssDNA chains at low grafting density and exhibits the well-known re-entrant phenomena of stretched chains with increased ionic strength at high grafting density. The binding results suggest that electrostatic attraction between the monomers and Mg 2 + plays the dominant role in defining the ion cloud around the ssDNA chains and generates a nearly-uniform ion distribution along the chains containing varying monomer sequences. These findings are in qualitative agreement with recent experimental results for Mg 2 + binding to surface-bound ssDNA.

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“…However, accurate all-atom molecular dynamics (AAMD) simulations can only be applied routinely to fairly small dendrimer-DNA systems, 11,12 since AAMD simulations are computationally expensive. On the other hand, widely used coarse-grained (CG) models, [13][14][15][16] which use bead-spring or bead-rod chains to model dsDNA as an effectively single-strand linear polyelectrolyte, can simulate binding and wrapping of DNA around a dendrimer. However since the diameter of dsDNA is almost the same as the radius of the dendrimer, the double-helix structure of DNA might be critical for local arrangement of the DNA along the dendrimer surface and thereby strongly affect the structure of the dendrimer-DNA complex.…”

Section: Introductionmentioning

confidence: 99%

Monte-Carlo simulations of PAMAM dendrimer–DNA interactions

Larson

2014

Soft Matter

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We use Monte Carlo simulations to determine the influence of poly(amido amine) (PAMAM) dendrimer size and charge on its interactions with double-stranded DNA conformation and interaction strength. To achieve a compromise between simulation speed and molecular detail, we combine the coarse-grained DNA model of de Pablo et al. which resolves each DNA base using three beads - and thereby retains the double-helix structure - with a dendrimer model with resolution similar to that of the DNA. The resulting predictions of the effects of dendrimer generation, dendrimer surface charge density, and salt concentration on dendrimer-DNA complexes are in agreement with both experiments and all-atom MD simulations. The model predicts that DNA wraps a fully charged G5 or G6 dendrimer at low salt concentration (10 mM) similarly to a histone octamer, and for the G5 dendrimer, DNA super helices with both handednesses occur. At salt concentrations above 50 mM, or when a high fraction of dendrimer surface charges are neutralized by acetylation, DNA adheres but does not compactly wrap the dendrimer, in agreement with experimental findings. We are also able to simulate pairs of dendrimers binding to the same DNA strand. Thus, our mesoscale simulation not only elucidates dendrimer-DNA interactions, but also provides a methodology for efficiently simulating chromatin formation and other cationic macroion-DNA complexes.

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Complexation between weakly basic dendrimers and linear polyelectrolytes: effects of grafts, chain stiffness, and pOH

Cited by 9 publications

References 60 publications

Interplay between Depletion and Electrostatic Interactions in Polyelectrolyte–Nanoparticle Systems

Interplay between Depletion and Electrostatic Interactions in Polyelectrolyte–Nanoparticle Systems

Quantifying Mg2+ Binding to ssDNA Oligomers: A Self-Consistent Field Theory Study at Varying Ionic Strengths and Grafting Densities

Monte-Carlo simulations of PAMAM dendrimer–DNA interactions

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