Structuring of counterions around dna double helix: a molecular dynamics study

TL;DR

This molecular dynamics study investigates how different alkali metal counterions interact with DNA's double helix, revealing distinct localization patterns and structural effects of Na+, K+, and Cs+ ions in various salt conditions.

Contribution

The paper provides detailed insights into the specific interactions and localization of Na+, K+, and Cs+ ions around DNA, highlighting the formation of a structured ionic system with Cs+ ions.

Findings

Na+ interacts from outside and via water molecules at DNA minor groove

K+ mainly localizes within the DNA grooves

Cs+ penetrates deeply and forms a structured ionic lattice

Abstract

Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been simulated. The systems have been considered in the regimes without excess salt and with different salts (0.5 M of NaCl, KCl or CsCl) added. The results have showed that the Na$^{+}$ counterions interact with the phosphate groups directly from outside of the double helix and via water molecules at the top edge of DNA minor groove. The potassium ions are mostly localized in the grooves of the double helix, and the cesium ions penetrate deeply inside the minor groove being bonded directly to the atoms of nucleic bases. Due to the electrostatic repulsion the chlorine ions tend to be localized at large distances from the DNA polyanion, but some Cl$^{-}$ anions have been detected near atomic groups of the double helix forming electrically neutral pairs with counterions already condensed on DNA. The DNA sites, where counterions are incorporated, are characterized by local changes of double helix structure. The lifetime of Na$^{+}$ and K$^{+}$ in complex with DNA atomic groups is less than 0.5 ns, while in the case of the cesium ions it may reach several nanoseconds. In this time scale, the Cs$^{+}$ counterions form a structured system of charges in the DNA minor groove that can be considered as ionic lattice.