Effects of Alkali-Metal Counterions on the Vibrational Dynamics of the DNA Hydration Shell.

Abstract

The effects of alkali-metal ions (Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺) on the vibrational dynamics of the DNA ion-hydration shell were studied through classical molecular dynamics simulations. As a result, the vibrational spectra of the DNA-water-salt systems were calculated within the framework of two approaches, using dipole-dipole and velocity-velocity autocorrelation functions. We dissect the effect of the individual compartments of the DNA double helix (minor groove, major groove, and phosphate groups) on the behavior of the systems. The obtained spectra have a different shape in the case of structure-making and structure-breaking ions. This difference becomes more prominent for the ions interacting with DNA, especially in the case of structure-breaking ions in the minor groove of the double helix. The obtained spectra of DNA do not show a significant effect of counterion type, except for Li⁺, which influences the vibrational modes of the DNA phosphates. The analysis of the spectra of water vibrations around ions revealed an isosbestic point at ∼70 cm^-1, which appears as a response to the confinement induced by interaction with the DNA double helix and counterions. The obtained results are important for understanding the structural and dynamical organization of the DNA ion-hydration shell.