Sergiy Perepelytsya | Searcharxiv

arXiv2022

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

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.

physics.bio-ph↗

arXiv2020

Positively and negatively hydrated counterions in molecular dynamics simulations of DNA double helix

The DNA double helix is a polyanionic macromolecule that in water solutions is neutralized by metal ions (counterions). The property of the counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na$^{+}$ counterions and negative hydration of K$^{+}$ and Cs$^{+}$ counterions, incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations. The results have shown that the dynamics of the hydration shell of counterions depends on region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions, localized in the minor groove of the double helix (about 50 ps for Na$^{+}$, and lower than 10 ps for K$^{+}$ and Cs$^{+}$). The estimated potentials of mean force for the hydration shells of the counterions show that the water molecules are constrained too strong, and, consequently, the effect of negative hydration for K$^{+}$ and Cs$^{+}$ counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.

q-bio.BM↗