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 . 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.
Highlights
The interaction between double-stranded B-DNA molecules has been extensively studied experimentally and theoretically [1,2,3] because of its importance in biology [4] and in DNA nanotechnology [5]
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 data obtained were fitted by two different theories of DNA–DNA interactions: the KL theory, and the homogeneously charged cylinders (HCC) theory
Summary
The interaction between double-stranded B-DNA molecules has been extensively studied experimentally and theoretically [1,2,3] because of its importance in biology [4] and in DNA nanotechnology [5]. The chirality of DNA molecules is expected to give rise to an asymmetry in interactions that depends on the handedness of the interaxial angle between two DNA molecules. Such asymmetry has been experimentally seen in DNA liquid crystals. Tilt-dependent electrostatic interactions between DNA molecules are important in biology and biophysics, as they may give rise to nontrivial effects in the behaviour of supercoiled DNA plasmids [15,16,17]
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