Low-frequency vibrations of water molecules in minor groove of the DNA double helix

TL;DR

This study models and analyzes the low-frequency vibrational dynamics of water molecules in the DNA minor groove, revealing specific frequencies and differences from bulk water, which are relevant for understanding DNA hydration mechanisms.

Contribution

A phenomenological model was developed to identify and characterize the vibrational modes of water molecules in the DNA minor groove, including effects of heavy water substitution.

Findings

Water vibrational frequencies range from 167 to 205 cm$^{-1}$.

Water vibrations are higher than DNA conformational vibrations.

Heavy water reduces vibrational frequencies by about 10 cm$^{-1}$.

Abstract

The dynamics of the structured water molecules in the hydration shell of the DNA double helix is of paramount importance for the understanding of many biological mechanisms. In particular, the vibrational dynamics of a water spine that is formed in the DNA minor groove is the aim of the present study. Within the framework of the developed phenomenological model, based on the approach of DNA conformational vibrations, the modes of H-bond stretching, backbone vibrations, and water translational vibrations have been established. The calculated frequencies of translation vibrations of water molecules vary from 167 to 205 cm$^{-1}$ depending on the nucleotide sequence. The mode of water vibrations higher than the modes of internal conformational vibrations of DNA. The calculated frequencies of water vibrations have shown a sufficient agreement with the experimental low-frequency vibrational spectra of DNA. The obtained modes of water vibrations are observed in the same region of the vibrational spectra of DNA as translation vibrations of water molecules in the bulk phase. To distinguish the vibrations of water molecules in the DNA minor groove from those in the bulk water, the dynamics of DNA with heavy water was also considered. The results have shown that in the case of heavy water the frequencies of vibrations decrease for about 10 cm$^{-1}$ that may be used in the experiment to identify the mode of water vibrations in the spine of hydration in DNA minor groove.