Effects of Alkali-Metal Counterions on the Vibrational\nDynamics of the DNA Hydration Shell

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