Molecular dynamics study of collective water vibrations in a DNA hydration shell

Abstract

The structure of DNA double helix is stabilized by water molecules and metal counterions that form the ion-hydration shell around the macromolecule. Understanding the role of the ion-hydration shell in the physical mechanisms of the biological functioning of DNA requires detailed studies of its structure and dynamics at the atomistic level. In the present work, the study of collective vibrations of water molecules around the DNA double helix was performed within the framework of classical all-atom molecular dynamics methods. Calculating the vibrational density of states, the vibrations of water molecules in the low-frequency spectra ranged from \(\sim\)30 to \(\sim\)300 \(\hbox {cm}^{-1}\) were analyzed for the case of different regions of the DNA double helix (minor groove, major groove, and phosphate groups). The analysis revealed significant differences in the collective vibrations behavior of water molecules in the DNA hydration shell, compared to the vibrations of bulk water. All low-frequency modes of the DNA ion-hydration shell are shifted by about 15–20 \(\hbox {cm}^{-1}\) towards higher frequencies, which is more significant for water molecules in the minor groove region of the double helix. The interactions of water molecules with the atoms of the macromolecule induce intensity decrease of the mode of hydrogen-bond symmetrical stretching near 150 \(\hbox {cm}^{-1}\), leading to the disappearance of this mode in the DNA spectra. The obtained results can provide an interpretation of the experimental data for DNA low-frequency spectra and may be important for the understanding of the processes of indirect protein–nucleic recognition.