Competitive substitution of hexammine cobalt(III) for Na+ and K+ ions in oriented DNA fibers

Korolev, Nikolay; Lyubartsev, Alexander P.; Rupprecht, A.; Nordenskiöld, Lars

doi:10.1002/1097-0282(200103)58:3<268::aid-bip1004>3.0.co;2-8

Cited by 28 publications

(16 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Here, the following values of the hard radii were used: R(K . These values are typical for hydrated ion radii used in a number of models and well reproduce thermodynamic properties and the features of ion distributions compared to all-atom simulations [12,65,66,82,85]. They also fit well the radius of the repulsive core region of the effective potentials derived within the IMC procedure, which is reflected in the corresponding RDFs in Figure S2 of the Supporting Material.…”

Section: Coarse-grained Dna Model: Large-scale Simulationssupporting

confidence: 72%

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

et al. 2014

Self Cite

View full text Add to dashboard Cite

Abstract:Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG) approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra-and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD) simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1-100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

show abstract

Section: Coarse-grained Dna Model: Large-scale Simulationssupporting

confidence: 72%

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

et al. 2014

Self Cite

View full text Add to dashboard Cite

show abstract

“…Similar data can also be obtained with varying degrees of sensitivity, convenience, completeness, and accuracy from atomic absorption spectroscopy, dye-indicator methods, and NMR line broadening [29,30,31 Grilley, 2006 #115].…”

Section: Characterizing the Ion Atmospherementioning

confidence: 91%

A repulsive field: advances in the electrostatics of the ion atmosphere

Chu

Bai

Lipfert

et al. 2008

Current Opinion in Chemical Biology

View full text Add to dashboard Cite

Summary The large electrostatic repulsion arising from the negatively-charged backbone of RNA molecules presents a large barrier to folding. Solution counterions assist in the folding process by screening this electrostatic repulsion. While early research interpreted the effect of these counterions in terms of an empirical ligand-binding model, theories based on physical models have supplanted them and revised our view of the roles that ions play in folding. Instead of specific ion-binding sites, most ions in solution interact inside an “ion atmosphere” – a fluctuating cloud of non-specifically associated ions surrounding any charged molecule. Recent advances in experiments have begun the task of characterizing the ion atmosphere, yielding valuable data that has revealed deficiencies in Poisson-Boltzmann theory, the most widely-used theory of the ion atmosphere. The continued development of experiments will help guide the development of improved theories, with the ultimate goal of understanding RNA folding and function and nucleic acid/protein interactions from a quantitative perspective.

show abstract

“…On the downside, all-atom MD simulations of such complicated systems require huge computational resources and majority of simulations aiming to describe details of the DNA solution phenomenology consist of 1–3 DNA molecules, where the focus is the counterion binding, effective interactions between DNA molecules, and/or azimuthal dependence of DNA-DNA interaction 26, 34–40 . Only recently it became feasible to set up a realistic all-atom MD simulation, with properly parameterized and tested molecular potentials that could be applied to a larger set of DNA molecules 41–43 , describing a condensed DNA array in the presence of counterions and salt, characterized by a single packing geometry, but as yet with only partial characterization of the DNA countercharge and solvent ordering.…”

Section: Introductionmentioning

confidence: 99%

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Zavadlav

Podgornik

Praprotnik

2017

Sci Rep

View full text Add to dashboard Cite

While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.

show abstract

Competitive substitution of hexammine cobalt(III) for Na+ and K+ ions in oriented DNA fibers

Cited by 28 publications

References 40 publications

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

A repulsive field: advances in the electrostatics of the ion atmosphere

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Contact Info

Product

Resources

About