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

by Ruggero Cortini, Xiaolin Cheng, Jeremy C Smith, Alexei Kornyshev
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Journal of Physics: Condensed Matter
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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 largescale
all-atom molecular dynamics simulations in explicit water and 150 mM sodium
chloride, to reconstruct the potential of mean force of two DNA oligomers 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 all our simulation data
well, and the fit yields the optimal value of the total 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 potential of mean force 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 of the order of 1kBT. In other
words, the effect of the detailed charge patterns are masked by thermal noise in the