Anion effect of Cl−, I−, and F− on counterions condensation within nucleic acid ion atmosphere

Abstract In the present work, molecular dynamics simulations have been carried out to study the anion effect on counterions distribution around the DNA double helix on the character of ion hydration. The simulated systems consisted of DNA fragment d(CGCGAATTCGCG) in water solution with the counterions and anions Cl−, I− or F−. Ion distribution and the characteristic binding sites of the counterions with DNA have been determined. The results show that due to the interaction with anions average number of counterions nearly DNA surface undergo changes. The amount of Na+ experienced a decline and the number of K+ experienced an increase with the change of Cl−, I−, and F− anion environment, while Na+ content remained at a high level compared with K+, anions are less present near DNA. Due to the dehydration effect, smaller Na + counterions can squeeze through the hydration shell of DNA to the bottom of the double helix grooves. Two counterions are mainly indirect binding DNA, which prefer to bind at the phosphate backbone compared to the major groove and negligible binding occurs in the minor groove. The K+ counterions show stronger ability to cluster with anions thus more likely to be shielded from DNA electrostatic field. The character of ion size, ion-DNA interaction, and the ion hydration establishes the correlation between the counterions and anions within nucleic acid ion atmosphere.