Low Temperature Physics: 48, 293 (2022); https://doi.org/10.1063/10.0009733
Fizika Nizkikh Temperatur: Volume 48, Number 4 (April 2022), p. 331-339    ( to contents , go back )

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

Sergiy Perepelytsya

Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, Kyiv 03143, Ukraine
E-mail: perepelytsya@bitp.kiev.ua

Oleksii Zdorevskyi

Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
pos Анотація:1263

Received December 09, 2021, published online February 25, 2022

Abstract

DNA is a 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 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 ± 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.

Key words: DNA, counterion condensation, polyelectrolyte, molecular dynamics.

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