Branch central strand

Figure 2. A stable DNA-branched junction. The junction shown is composed of four strands of DNA, labeled with Arabic numerals arms are labeled with Roman numerals. The 3 end of each strand is indicated by the half-arrows. Each strand is paired with two other strands to form a double helical arm. There is no homologous twofold sequence symmetry flanking the central branch point, thereby stabilizing its position.

Figure 11. Antijunctions and mesojunctions. (a) A 949 knot drawn in a DNA context. Each of the nodes of this knot is shown to be formed from a half-turn of double helical DNA. The polarity of the knot is indicated by the arrowheads passing along it. Various enclosed areas contain symbols indicating the condensation of nodes to form figures. The curved double-headed arrow indicates the condensation of two half-turns into a full turn, the solid triangle indicates a three-arm branched junction, the empty square indicates a 4-strand antijunction, and the shaded square is a four-strand mesojunction. (b) Schematic drawings of 3-strand and 4-strand junctions, antijunctions, and mesojunctions shown as the helical arrangements that can flank a triangle or a square. Each polygon is formed from strands of DNA that extend beyond the vertices in each direction. The arrowheads indicate the 3 ends of the strands. The vertices correspond to the nodes formed by a half-turn of double helical DNA. Base pairs are represented by lines between antiparallel strands. Thin double-headed arrows perpendicular to the base pairs represent the axis of each helical half-turn. The lines perpendicular to the helix axes terminating in ellipses represent the central dyad axes of the helical half-turns. The complexes 33 and 44 correspond to conventional branched junctions. The complex 40 is a 4-strand antijunction. The complexes on the bottom row are mesojunctions, which contain a mix of the two orientations of helix axes.

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