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

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