Reentrant Behavior of Divalent-Counterion-Mediated DNA-DNA Electrostatic Interaction

Lee, SeIl; Le, Tung T.; Nguyen, Toan T.

doi:10.1103/physrevlett.105.248101

Cited by 10 publications

(5 citation statements)

References 21 publications

(22 reference statements)

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“…More data at higher MgCl 2 concentrations is needed to obtain reliable fitting parameters for this case. In fact, the value c Z,0 104 mM obtained from the computer simulation of [26] is nearly twice as large as our semi−empirical results. This demonstrates again that this concentration is very sensitive to the exact calculation of the counterion correlation energy μ cor .…”

Section: Fitting Of Experiments Of Dna Ejection From Bacteriophages Ansupporting

confidence: 70%

“…It should be mentioned that Mg +2 counterions have been shown experimentally to condense DNA in another confined system: the DNA condensation in two dimension [25]. Results from our computer simulations in Section 5 (see also [26,27]), also show that if the lateral motion of DNA is restricted, divalent counterions can induced DNA condensation. The strength of DNA-DNA attraction energy mediated by divalent counterions is comparable to the theoretical results.…”

Section: Introductionmentioning

confidence: 50%

“…Only in the confinement of the viral capsid can this attraction effect appear in the ejection process. It should be mentioned that computer simulations of DNA condensation by idealized divalent counterions [26,27] show a weak shortrange attraction comparable to our μ DNA . This suggests that in the presence of divalent counterions, electrostatic interaction are an important (if not dominant) contribution to DNA-DNA short range interactions inside viral capsid.…”

Section: Fitting Of Experiments Of Dna Ejection From Bacteriophages Anmentioning

confidence: 99%

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Strongly correlated electrostatics of viral genome packaging

Nguyen

2013

J Biol Phys

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The problem of viral packaging (condensation) and ejection from viral capsid in the presence of multivalent counterions is considered. Experiments show divalent counterions strongly influence the amount of DNA ejected from bacteriophage. In this paper, the strong electrostatic interactions between DNA molecules in the presence of multivalent counterions is investigated. It is shown that experiment results agree reasonably well with the phenomenon of DNA reentrant condensation. This phenomenon is known to cause DNA condensation in the presence of tri-or tetra-valent counterions. For divalent counterions, the viral capsid confinement strongly suppresses DNA configurational entropy, therefore the correlation between divalent counterions is strongly enhanced causing similar effect. Computational studies also agree well with theoretical calculations.

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Section: Fitting Of Experiments Of Dna Ejection From Bacteriophages Ansupporting

confidence: 70%

Section: Introductionmentioning

confidence: 50%

Section: Fitting Of Experiments Of Dna Ejection From Bacteriophages Anmentioning

confidence: 99%

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Strongly correlated electrostatics of viral genome packaging

Nguyen

2013

J Biol Phys

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“…Like-charged attraction can lead to nanoparticle or polymer condensation and formation of charged complexes or crystals. The factors that determine whether the net interaction is repulsive or attractive include the surface charge density, the flexibility of the interface or chains, the structure and charge density of the multivalent counterions, the solution concentrations of the nanoparticles/molecules and salts, and the geometry of the interfaces: spherical (colloidal particles, for example), chain-coated particles (for example, DNA-coated nanoparticles), cylindrical/rod-like (like microtubules or actin), flat (charged lipid bilayers), semiflexible chains (like DNA), or flexible chains (like sodium polystyrenesulfonate). − …”

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confidence: 99%

Crystallization, Reentrant Melting, and Resolubilization of Virus Nanoparticles

et al. 2017

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Crystallization is a fundamental and ubiquitous process that is well understood in the case of atoms or small molecules, but its outcome is still hard to predict in the case of nanoparticles or macromolecular complexes. Controlling the organization of virus nanoparticles into a variety of 3D supramolecular architectures is often done by multivalent ions and is of great interest for biomedical applications such as drug or gene delivery and biosensing, as well as for bionanomaterials and catalysis. In this paper, we show that slow dialysis, over several hours, of wild-type Simian Virus 40 (wt SV40) nanoparticle solution against salt solutions containing MgCl, with or without added NaCl, results in wt SV40 nanoparticles arranged in a body cubic center crystal structure with Im3m space group, as a thermodynamic product, in coexistence with soluble wt SV40 nanoparticles. The nanoparticle crystals formed above a critical MgCl concentrations. Reentrant melting and resolubilization of the virus nanoparticles took place when the MgCl concentrations passed a second threshold. Using synchrotron solution X-ray scattering we determined the structures and the mass fraction of the soluble and crystal phases as a function of MgCl and NaCl concentrations. A thermodynamic model, which balances the chemical potentials of the Mg ions in each of the possible states, explains our observations. The model reveals the mechanism of both the crystallization and the reentrant melting and resolubilization and shows that counterion entropy is the main driving force for both processes.

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“…In this paper, as a first step in such direction, we present a Grand canonical Monte-Carlo (GCMC) simulation of electrolyte solutions for different salinity expanding upon a preliminary study [11]. The Grand-Canonical Monte-Carlo method was developed and used in several recent papers in our group to study the condensation of DNA inside bacteriophages in the presence of mixture of different salts, MgSO4, MgCl2, NaCl [12,13,14,15]. However, detail of the method was never presented, only the simulation results of DNA system were shown.…”

Section: Introduction mentioning

confidence: 99%

Size Effect in Grand-canonical Monte-Carlo Simulation of Solutions of Electrolyte

Duc

2019

MaP

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A Grand-canonical Monte-Carlo simulation method is investigated. Due to charge neutrality requirement of electrolyte solutions, ions must be added to or removed from the system in groups. It is then implemented to simulate solution of 1:1, 2:1 and 2:2 salts at different concentrations using the primitive ion model. We investigate how the finite size of the simulation box can influence statistical quantities of the salt system. Remarkably, the method works well down to a system as small as one salt molecule. Although the fluctuation in the statistical quantities increases as the system gets smaller, their average values remain equal to their bulk value within the uncertainty error. Based on this knowledge, the osmotic pressures of the electrolyte solutions are calculated and shown to depend linearly on the salt concentrations within the concentration range simulated. Chemical potential of ionic salt that can be used for simulation of these salts in more complex system are calculated. Keywords: GCMC, electrolyte solution simulation, primitive ion model, finite size effect.

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Reentrant Behavior of Divalent-Counterion-Mediated DNA-DNA Electrostatic Interaction

Cited by 10 publications

References 21 publications

Strongly correlated electrostatics of viral genome packaging

Strongly correlated electrostatics of viral genome packaging

Crystallization, Reentrant Melting, and Resolubilization of Virus Nanoparticles

Size Effect in Grand-canonical Monte-Carlo Simulation of Solutions of Electrolyte

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