Dynamics of K + counterions around DNA double helix in the external electric field: A molecular dynamics study
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THE EUROPEAN PHYSICAL JOURNAL E
Regular Article
Dynamics of K+ counterions around DNA double helix in the external electric field: A molecular dynamics study O.O. Zdorevskyia and S.M. Perepelytsya Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14-b, Metrolohichna Str., Kiev, 03143, Ukraine Received 26 May 2020 / Received in final form 4 September 2020 / Accepted 5 November 2020 Published online: 3 December 2020 c EDP Sciences / Societ` a Italiana di Fisica / Springer-Verlag GmbH Germany, part of Springer Nature, 2020 Abstract. The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study was performed for the system of DNA double helix with neutralizing K+ counterions and for the system of KCl salt solution in an external electric field of different strength (up to 32 mV/˚ A). The analysis of ionic conductivities of these systems has shown that the counterions around the DNA double helix are slowed down compared with the KCl salt solution. The calculated values of ion mobility are within (0.05–0.4) mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K+ counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30 mV/˚ A the double helix undergoes a phase transition from a double-stranded to a single-strand state.
1 Introduction The DNA macromolecule in a water solution is a strong polyelectrolyte inducing a condensation of small mobile positive ions (counterions) from the bulk to a diffuse layer around the double helix [1, 2]. The ionic cloud screens the negatively charged phosphate groups of DNA backbone reducing the electrostatic repulsion of the opposite strands of the double helix that is determinative for its stabilization [3]. In the cell nuclei the part of electrostatic charge of the DNA macromolecule is neutralized by the positively charged molecular groups of histone proteins, while the counterions screen the rest of the negative charge of the double helix [4,5]. The structure and dynamics of the cloud of counterions are governed by strong electrostatic fields, produced by DNA and protein macromolecules. Therefore, the dynamical response of counterions on the external electrostatic field should be studied to understand the physical mechanisms of the DNA-counterion interaction in the real systems. The counterions around the DNA double helix are localized within a layer of about 7 ˚ A thickness [1]. The main Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1
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