Figure 3. Distances characterizing the interaction between Mg²⁺ and DNA during the MD simulations.

The distances between Mg²⁺ and the electronegative atoms N7(A₂₂ and G₂₃), O6(G₂₃) and O2P(p₂₂) belonging to the p₂₂A₂₂p₂₃G₂₃ fragment were extracted from S1. Mg²⁺ interacts with A₂₂ and G₂₃ via its first hydration shell for roughly 20 ns, as shown by the values of the distances d(Mg²⁺ – N7(A₂₂)), d(Mg²⁺ – N7(G₂₃)), and d(Mg²⁺ – O6(G₂₃)). O2P(p₂₂) is transitorily close to Mg²⁺. Short Mg²⁺ – O2P(A₂₂) distances are associated with p₂₂ in BII (BI in blue, BII in red). Identical interaction patterns are observed in S2 and S3.