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

TL;DR

This study combines theoretical modeling and molecular dynamics simulations to analyze the distribution and trapping of counterions around DNA, revealing limits on ion localization inside the double helix and validating the model with simulation data.

Contribution

It introduces a model for counterion distribution around DNA and confirms its predictions with molecular dynamics simulations, advancing understanding of DNA-ion interactions.

Findings

Number of counterions inside DNA limited to about 0.4 per phosphate.

Simulations show approximately 0.22 counterions trapped in grooves per phosphate.

Model accurately predicts counterion localization around DNA.

Abstract

DNA is strong polyelectrolyte macromolecule making metal ions (counterions) condense to a cloud around the double helix. The counterions may be localized outside the macromolecule and inside the minor and major grooves of the double helix. In the present work, the distribution of condensed counterions between inner and outer regions of DNA has been studied using the approaches of counterion condensation theory. The results have shown that the number of counterions trapped inside the macromolecule should be greater than 0.16 per one phosphate group. The maximal number of counterions that may be localized inside the DNA double helix is limited to about 0.4 per one phosphate group and it is much lower than the total number of condensed counterions. To analyze the structure of counterion cloud the molecular dynamics simulations of \emph{B}-DNA with K$^{+}$ counterions have been performed. The obtained number of the counterions trapped inside the grooves of the double helix is about 0.22$\pm$0.06 per one phosphate group that agree with the model estimations. The developed model describes general features of the structure of counterion cloud around DNA and is able to predict the number of counterions inside the grooves of the double helix.