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Abstract
Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: localization of the slowest hydration water molecules---in the groove in DNA, next to phosphates in RNA--- and a markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules, but is caused by both a larger excluded volume and a stronger initial H-bond next to OR, which can be linked to different phosphate orientations in A-form double helical RNA.
Supplementary materials
Title
Supporting Information
Description
Supporting Information with computational details, additional analyses of the nucleic acid structures and jump times, and ion density maps.
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SI files
Description
All input, parameter files, reorientation and jump maps are shared in an archive folder SI-files.zip
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Supplementary weblinks
Title
Two 100 ns NVT molecular dynamics simulations of dsDNA and dsRNA "GGGG" 18-mers (GCGGGGGGGGGGGGGGGC)
Description
Supporting information for "Molecular origin of distinct hydration dynamics in double helical DNA and RNA sequences" by E. Frezza, D. Laage and E. Duboué-Dijon.
Two 100 ns-long NVT molecular dynamics simulation: one of dsDNA "GGGG" 18-mer (GCGGGGGGGGGGGGGGGC) and one of the analogous dsRNA. The nucleic acid is explicitly solvated in water and neutralized with 0.15M KCl. Simulations were performed using the Gromacs 5 software. DNA is described with the Amber 99SB-ILDN force field with the BSC0 modifications, RNA is described with the Amber 99SB-ILDN force field with the BSC0 and χOL3 modifications, the SPC/E force field is used for water, and the Joung Cheatham paraeters for ions. The shared coordinates are saved every 500fs, twice less frequently than the original trajectories used for the publication, to reduce the size of the shared dataset below the allowed size limit.
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