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Polymers 2014, 6(6), 1655-1675; doi:10.3390/polym6061655
Article

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

1
, 1
, 2,*  and 1,*
Received: 15 April 2014; in revised form: 15 May 2014 / Accepted: 18 May 2014 / Published: 30 May 2014
(This article belongs to the Special Issue Polyelectrolytes 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.
Keywords: DNA; coarse-grained model; molecular dynamics; persistence length DNA; coarse-grained model; molecular dynamics; persistence length
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Korolev, N.; Luo, D.; Lyubartsev, A.P.; Nordenskiöld, L. A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo. Polymers 2014, 6, 1655-1675.

AMA Style

Korolev N, Luo D, Lyubartsev AP, Nordenskiöld L. A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo. Polymers. 2014; 6(6):1655-1675.

Chicago/Turabian Style

Korolev, Nikolay; Luo, Di; Lyubartsev, Alexander P.; Nordenskiöld, Lars. 2014. "A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo." Polymers 6, no. 6: 1655-1675.


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