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DNA is strong polyelectrolyte macromolecule making metal ions (counterions)condense to a cloud around the double helix. The counterions may be localizedoutside the macromolecule and inside the minor and major grooves of the doublehelix. In the present work, the distribution of condensed counterions betweeninner and outer regions of DNA has been studied using the approaches ofcounterion condensation theory. The results have shown that the number ofcounterions trapped inside the macromolecule should be greater than 0.16 perone phosphate group. The maximal number of counterions that may be localizedinside the DNA double helix is limited to about 0.4 per one phosphate group andit is much lower than the total number of condensed counterions. To analyze thestructure of counterion cloud the molecular dynamics simulations of\emph{B}-DNA with K$^{+}$ counterions have been performed. The obtained numberof the counterions trapped inside the grooves of the double helix is about0.22$\pm$0.06 per one phosphate group that agree with the model estimations.The developed model describes general features of the structure of counterioncloud around DNA and is able to predict the number of counterions inside thegrooves of the double helix.

Counterion atmosphere around DNA double helix: trapping of counterions at the nanoscale