Figure 1.

Overview of the DNA origami rectangle and atomistic MD simulations with various counterions. (a) DNA origami design considered in the MD simulations, with the scaffold strand shown in gray and the staple strands in color. (b–f) Snapshots of the final configurations of the Sodium, Mixed, Magnesium, PLL-10, and Spermine simulation, respectively, with the DNA origami shown in gray, water in light blue, and Na⁺, Mg²⁺, K₁₀, and Spm⁴⁺ in blue, red, yellow, and green, respectively. For each structure, both a top and side view are shown. (g) Root-mean-square deviation (RMSD) of the DNA backbone atoms from their initial positions as a function of time for the five simulations. (h) Aspect ratio of the DNA origami rectangle as a function of time for the five simulations. The inset shows the initial aspect ratio. (i) Fraction of DNA charge compensated by ions within 5 Å of DNA atoms for the Sodium, Mixed, Magnesium, PLL-10, and Spermine simulations as a function of time.