Interaction of double-stranded DNA with a nanosphere: a coarse-grained molecular dynamics simulation study

Cao, Qi; Zuo, Chao; Yan, Ma; Li, Lujuan; Zhou, Zhifang

doi:10.1039/c0sm00512f

Cited by 26 publications

(28 citation statements)

References 44 publications

(70 reference statements)

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“…A number of theoretical coarse-graining models of DNA [24][25][26][27][28][29][30][31][32][33][34][35] and chromatin [13][14][15][36][37][38][39][40][41][42][43][44][45][46][47][48][49] have been reported recently. In recent works from the Papoian group, a CG model of a single DNA molecule was developed [24][25][26]50].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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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.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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“…A number of coarse-grained models of DNA [47]–[51] and chromatin [43], [52]–[68] have been developed recently (reviewed in [16]). Most of the chromatin models aim at describing and understanding the nature of the folded 30 nm fibre chromatin structure.…”

Section: Introductionmentioning

confidence: 99%

An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions

et al. 2013

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In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs). The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar) plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K+), divalent (Mg2+) or trivalent (Co(NH3)6 3+) cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K+, to partial aggregation with Mg2+ and to strong mutual attraction of all 10 NCPs in the presence of CoHex3+. The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.

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“…[12][13][14][15][16][17][18][19][20][21][22][23][24][25] An important aspect of PE adsorption is the charge inversion, that is, the total amount of charges on adsorbed PE chains overcompensates that of the surface charges of the object. Other interesting issues regarding the PE adsorption, such as the critical condition for the adsorption, the thickness of the polymer layer, the addition of the salt ions, and the difference between planar and curved (cylindrical, spherical) charged objects, have also attracted the research attention.…”

Section: Introductionmentioning

confidence: 99%

The numerical study of the adsorption of flexible polyelectrolytes with the annealed charge distribution onto an oppositely charged sphere by the self-consistent field theory

Tong

2013

The Journal of Chemical Physics

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The adsorption of flexible polyelectrolytes (PEs) with the annealed charge distribution onto an oppositely charged sphere immersed in a PE solution is studied numerically with the continuum self-consistent field theory. The numerical study reveals interesting scaling relationships between the boundary layer thickness and the surface charge density of the sphere as well as the degree of ionization of the monomers of the PE chains in the bulk solution. The dependences of the degree of charge compensation of the total amount of charges on adsorbed PE chains over the surface charges upon various system parameters are investigated. In particular, the effect of the radius of the charged sphere on the degree of charge compensation is carefully examined. The numerical study indicates that the curvature effect is closely related to the surface electric potential of the charged sphere. Moreover, in this study of the adsorption of PEs with the annealed charge distribution, a comparison with the corresponding case for PEs with the smeared charge distribution in terms of the boundary layer scaling law and the degree of charge compensation is also presented.

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Interaction of double-stranded DNA with a nanosphere: a coarse-grained molecular dynamics simulation study

Cited by 26 publications

References 44 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

An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions

The numerical study of the adsorption of flexible polyelectrolytes with the annealed charge distribution onto an oppositely charged sphere by the self-consistent field theory

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