The effects of positive and negative hydrationof counterions (Na^{+ and Cs^{+} ) incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics approach . The results show that the dynamics of the hydration shell of counterions depends on region of ion localization around the macromolecule. The longest residence times have been observed for water molecules near the counterionsthat are localized in the minor groove of the double helix : about 30 ps in the case of Na^{+ K^{+} and Cs^{+} counterions. In the major groove and outside the double helix it is essentially lower. The counterions constrain water molecules too strong, and as the result the effect of negative hydration for K^{+} and Cs^{+} counterions was not observed in the simulations. The analysis show that the effects of counterion hydration may be described better by using the water models with lower dipole moments.
The DNA double helix is a polyanionic macromolecule that in water solutions is neutralized by metal ions (counterions). The property of the counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na^{+ and Cs^{+} counterions, incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations . The results have shown that the dynamics of the hydration shell of counterions depends on region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions, localized in the minor groove of the double helix (about 50 ps for Na^{+ K^{+} and Cs^{+} ). The estimated potentials of mean force for the hydration shells of the counterions show that the water molecules are constrained too strong, and , consequently, the effect of negative hydration for K^{+} and Cs^{+} counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.
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