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:10.1088/1361-648X/aa4e68

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

Journal Article · Mon Jan 16 00:00:00 EST 2017 · Journal of Physics. Condensed Matter

DOI:https://doi.org/10.1088/1361-648X/aa4e68· OSTI ID:1339311

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

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 $$1{{k}_{\text{B}}}T$$ . 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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725

OSTI ID:: 1339311

Alternate ID(s):: OSTI ID: 1339312; OSTI ID: 1346650

Journal Information:: Journal of Physics. Condensed Matter, Journal Name: Journal of Physics. Condensed Matter Vol. 29 Journal Issue: 8; ISSN 0953-8984

Publisher:: IOP PublishingCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 8 works

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

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