Fig. 7. Cation distributions around the MixRNA duplex computed from simulations.

(A to C) A snapshot from each simulation setup where only the cations in the vicinity of the RNA are shown with their first solvation shell water molecules. (A) 400 mM KCl, (B) 100 mM NaCl, and (C) 10 mM MgCl₂. The average distribution of cations is monitored by cylindrical concentration profiles along the long axis of dsRNA. The solid line represents c(ρ) as a function of the distance from the central axis of the duplex with the same order. (D) KCl, (E) NaCl, and (F) MgCl₂. 3D ion density plots colored from white (low) to red to green (high) and shown in the same order as (G) KCl, (H) NaCl, and (I) MgCl₂, respectively. (J) Radial distribution function of K⁺ ions from the duplex surface. Different colors represent correlation of cations with different parts of the duplex: (black) with the whole duplex atoms, (red) with major groove, and (blue) with backbone phosphate. The inset in (J) depicts dehydrated (left, first peak) and hydrated (right, second peak) bound states. (K to L) Same as (J), but this time for Na⁺ and Mg²⁺, respectively.