Ionic distribution around simple B-DNA models. III. The effect of ionic charge

Abascal, J. L. F.; Montoro, J. C. Gil

doi:10.1063/1.1342035

Cited by 30 publications

(38 citation statements)

References 43 publications

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“…For example, a maximum in ion density is observed at about 8 Å from the DNA axis, corresponding to a high probability for counterions to be inside the DNA grooves. [38] On larger distances from the DNA, the ion distribution, computed in MD simulations, became more similar to that calculated in the PB theory, or obtained in continuum solvent simulations. In addition, the integral charge for Na + ions turned out to be very similar already on distances greater than 12 Å from the DNA surface (Fig.…”

Section: Specific Binding Of Ionsmentioning

confidence: 60%

“…[36] Enhanced concentration of counterions in the grooves (with stronger effect in the minor groove) has been observed also in several works. [37,38] However, distribution of counterions far from the DNA depends only weakly on the structure of the DNA surface.…”

Section: Effect Of Specific Distribution Of Chargesmentioning

confidence: 99%

“…Other studies of the ion competition effects are reported in a number of more recent MC simulations. [38,48,49] It was shown that the PB approximation underestimates binding of higher-valency ions and that this underestimation increases with ion valency. [38,45] In the case of concentrated polyelectrolyte systems (e.g., oriented DNA fibers in equilibrium with a bulk electrolyte solution), the situation is different.…”

Section: Ion Competitionmentioning

confidence: 99%

“…[38,48,49] It was shown that the PB approximation underestimates binding of higher-valency ions and that this underestimation increases with ion valency. [38,45] In the case of concentrated polyelectrolyte systems (e.g., oriented DNA fibers in equilibrium with a bulk electrolyte solution), the situation is different. The simulation cell, in this case, cannot include the ''bulk'' solution, so the concentration of the ions in the bulk is not directly known.…”

Section: Ion Competitionmentioning

confidence: 99%

“…The effects caused by a specific distribution of charges on the polyion surface were studied in a number of works [13,31,[35][36][37][38] with applications to DNA. Quite evidently, a different structure of the charge distribution on the polyion may cause a rather different distribution of the ion density in the close vicinity of the polyion.…”

Section: Effect Of Specific Distribution Of Chargesmentioning

confidence: 99%

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Molecular Simulations of DNA Counterion Distributions

Lyubartsev¹

2004

Dekker Encyclopedia of Nanoscience and Nanotechnology, Second Edition - Six Volume Set (Print Version)

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Section: Specific Binding Of Ionsmentioning

confidence: 60%

Section: Effect Of Specific Distribution Of Chargesmentioning

confidence: 99%

Section: Ion Competitionmentioning

confidence: 99%

Section: Ion Competitionmentioning

confidence: 99%

Section: Effect Of Specific Distribution Of Chargesmentioning

confidence: 99%

See 3 more Smart Citations

Molecular Simulations of DNA Counterion Distributions

Lyubartsev¹

2004

Dekker Encyclopedia of Nanoscience and Nanotechnology, Second Edition - Six Volume Set (Print Version)

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Titration of poly(dA‐dT) · poly(dA‐dT) in solution at variable NaCl concentration

et al. 2004

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CD and uv absorption data showed that high molecular weight poly(dA-dT) . poly(dA-dT), at 298 K, undergoes an acid-induced transition from B-double helix to random coil in NaCl solutions of different concentrations, ranging from 0.005 to 0.600M. Similarly, titration of the polynucleotide with a strong base causes duplex-to-single strands transition. The base- and acid-induced transitions were both reversible by back-titration (with an acid or, respectively, with a base): the apparent pKa were the same in both directions. However, the number of protons per titratable site (adenine N1) required to reach half-denaturation was in great excess over the stoichiometric value; to a much larger extent, the same effect was observed also for the deprotonation of the N3H sites of thymine. Moreover, in the basic denaturation experiments, at low salt concentrations ([NaCl]< or =0.300M) less acid than calculated was needed to back-titrate the base excess to half-denaturation. Both effects could be qualitatively justified on the basis of the counterion condensation theory of polyelectrolytes and considering the energy barrier created by the negatively charged phosphodiester groups to the penetration of the OH- ions inside the double helix and the screening effect of the Na+ ions on such charges, in the deprotonation experiments.

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A new outer boundary formulation and energy corrections for the nonlinear Poisson–Boltzmann equation

Boschitsch

Fenley

2007

J Comput Chem

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The nonlinear Poisson-Boltzmann equation (PBE) has been successfully used for the prediction of numerous electrostatic properties of highly charged biopolyelectrolytes immersed in aqueous salt solutions. While numerous numerical solvers for the 3D PBE have been developed, the formulation of the outer boundary treatments used in these methods has only been loosely addressed, especially in the nonlinear case. The de facto standard in current nonlinear PBE implementations is to either set the potential at the outer boundaries to zero or estimate it using the (linear) Debye-Hückel (DH) approximation. However, an assessment of how these outer boundary treatments affect the overall solution accuracy does not appear to have been previously made. As will be demonstrated here, both approximations can, under certain conditions, produce completely erroneous estimates of the potential and energy salt dependencies. A related concern for calculations carried out on grids of finite extent (e.g., all current finite difference and finite element implementations) is the contribution to the energy and salt dependence from the exterior region outside the computational grid. This too is shown to be significant, especially at low salt concentration where essentially all of the contributions to the excess osmotic pressure and ion stress energies originate from this exterior region. In this paper the authors introduce a new outer boundary treatment that is valid for both the linear and nonlinear PBE. The authors also formulate energy corrections to account for contributions from outside the computational domain. Finally, the authors also consider the effects of general ion exclusion layers upon biomolecular electrostatics. It is shown that while these layers tend to increase the surface electrostatic potential, under physiological salt conditions and high net charges their effect on the excess osmotic pressure term, which is a measure of the salt dependence of the total electrostatic free energy, is weak. To facilitate presentation and allow very fine resolutions and/or large computational domains to be considered, attention is restricted to the 1D spherically symmetric nonlinear PBE. Though geometrically limited, the modeling principles nevertheless extend to general PBE solvers as discussed in the Appendix. The 1D model can also be used to benchmark and validate the salt effect prediction capabilities of existing PBE solvers.

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Ionic distribution around simple B-DNA models. III. The effect of ionic charge

Cited by 30 publications

References 43 publications

Molecular Simulations of DNA Counterion Distributions

Molecular Simulations of DNA Counterion Distributions

Titration of poly(dA‐dT) · poly(dA‐dT) in solution at variable NaCl concentration

A new outer boundary formulation and energy corrections for the nonlinear Poisson–Boltzmann equation

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