Molecular origin of distinct hydration dynamics in double helical DNA and RNA sequences

28 February 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

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.

Keywords

Solvation
Molecular Dynamics
Nucleic Acids

Supplementary materials

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Description
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Supporting Information
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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
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All input, parameter files, reorientation and jump maps are shared in an archive folder SI-files.tar.gz
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Supplementary weblinks

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