Antijunctions and Mesojunctions
Each polygon (triangle or square) is flanked by cyan, green, red (and magenta) 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 approximately a half-turn of double helical DNA. Base pairs are represented by aqua lines between antiparallel strands. Orange, double-arrowheaded lines perpendicular to the base pairs represent the axis of each helix. Purple lines (ending in lens-shaped figures) perpendicular to the helix axes represent the local dyad axes of the DNA half-turn. The complexes 33 and 44 correspond to conventional branched junctions. Their helix axes are all pointing towards the center of the triangle or square along the bisectors of the angles of the polygons ('radial'). The complex 40 is a 4-strand antijunction, in which each helix axis ideally is perpendicular to the angular bisectors ('circumferential'). Note that when the helix axes are radial, the dyad axes are circumferential, and vice versa. The complexes are named by a large number which indicates the number of double helical segments, a subscript which indicates how many of them are pointed along the angular bisectors, and a presuperscript (if necessary) enumerating different members of a class otherwise undifferentiated by the first two numbers. The complexes on the bottom row contain a mix of the two orientations of helix axes. The complex 31 contains one radial helix axis and two circumferential axes. The complexes 142 and 242, each contain a pair of radial helix axes and a pair of circumferential axes, but the arrangement is different between them: 142 contains alternating radial and circumferential axes, whereas 242 contains two radial axes on the right of the square and two circumferential axes on the left.
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