The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

doi:http://dx.doi.org/10.1088/1361-648X/aa4e68

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

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Cortini R, Cheng X, Smith JC. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations. J Phys Condens Matter. 2017 Mar 1;29(8):084002. DOI: 10.1088/1361-648X/aa4e68. Epub 2017 Jan 16

Abstract

Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of [Formula: see text]. Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.