Figure 1.

(A) and (B) OxDNA configurations for a single Holliday junction at 0.5 M salt that are representative of (A) the left-handed global free-energy minimum (ϕ = 95.5°, θ = 2.5°) and (B) an anti-parallel junction (ϕ = 180°, θ = 5°). (i) and (ii) provide perpendicular views of the configurations. In both cases the green and purple strands cross from one double helix to another, while the blue and red strands carry straight on along their double helix. (A)(iii) and (B)(iii) provide schematics of a left-handed parallel and an anti-parallel junction, respectively. (C) The Holliday-junction free-energy landscape as a function of ϕ and θ. One-dimensional free-energy profiles for ϕ and θ are also shown. The full free-energy profile for θ is shown as a solid blue line, while the dashed red line is for the subregion 160° ≤ ϕ ≤ 180°, shaded grey in the free-energy landscape. ϕ = (ϕ₁ + ϕ₂)/2 is a measure of the chiral twist of the junction, where ϕ₁ and ϕ₂ are the angles between the arms as indicated in (A)(i). θ = (θ₁ + θ₂)/2 is the average angle between each arm and the plane of the junction, as indicated in (B)(ii). The plane of the junction, represented by the dotted line in (B)(ii), is perpendicular to the plane of the paper and passes through the midpoints of the exchanging strands. The temperature used was 296.15 K.