Computational Study of Phosphate Vibrations as Reporters of DNA Hydration

The sensitivity of the phosphate asymmetric stretch vibrational frequency to DNA hydration was investigated with molecular dynamics (MD) simulations and a spectroscopic map relating the vibrational frequency to the electrostatics of its environment. 95% of the phosphate vibrational frequency shift in fully hydrated DNA was due to water within two hydration layers. The phosphate vibration was relatively insensitive to water in the major and minor grooves and to the sodium counterions but was enormously sensitive to water interacting with the DNA backbone. Comparisons to experimental measurements on DNA as a function of relative humidity suggest that one water molecule per phosphate group likely persists at the lowest values of the relative humidity. Finally, the calculated spectral diffusion dynamics show that water in the vicinity of the DNA backbone is slowed by a factor of ∼5, in agreement with NMR and solvation dynamics experiments, as well as previous MD simulations.