The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations
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 $$1{{k}_{\text{B}}}T$$ . 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.
- Authors:
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1339311
- Alternate Identifier(s):
- OSTI ID: 1339312; OSTI ID: 1346650
- Grant/Contract Number:
- AC02-05CH11231; AC05-00OR22725
- Resource Type:
- Published Article
- Journal Name:
- Journal of Physics. Condensed Matter
- Additional Journal Information:
- Journal Name: Journal of Physics. Condensed Matter Journal Volume: 29 Journal Issue: 8; Journal ID: ISSN 0953-8984
- Publisher:
- IOP Publishing
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; DNA–DNA interactions; all-atom molecular dynamics simulations; Umbrella sampling; Kornyshev-Leikin theory
Citation Formats
Cortini, Ruggero, Cheng, Xiaolin, and Smith, Jeremy C. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations. United Kingdom: N. p., 2017.
Web. doi:10.1088/1361-648X/aa4e68.
Cortini, Ruggero, Cheng, Xiaolin, & Smith, Jeremy C. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations. United Kingdom. https://doi.org/10.1088/1361-648X/aa4e68
Cortini, Ruggero, Cheng, Xiaolin, and Smith, Jeremy C. Mon .
"The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations". United Kingdom. https://doi.org/10.1088/1361-648X/aa4e68.
@article{osti_1339311,
title = {The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations},
author = {Cortini, Ruggero and Cheng, Xiaolin and Smith, Jeremy C.},
abstractNote = {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.},
doi = {10.1088/1361-648X/aa4e68},
journal = {Journal of Physics. Condensed Matter},
number = 8,
volume = 29,
place = {United Kingdom},
year = {Mon Jan 16 00:00:00 EST 2017},
month = {Mon Jan 16 00:00:00 EST 2017}
}
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