Double Crossover Molecules
The structures shown are named by the acronym describing their basic characteristics. All names begin with 'D' for double crossover. The second character refers to the relative orientations of their two double helical domains, 'A' for antiparallel and 'P' for parallel. The third character refers to the number (modulus 2) of helical half-turns between crossovers, 'E' for an even number and 'O' for an odd number. A fourth character is needed to describe parallel double crossover molecules with an odd number of helical half-turns between crossovers. The extra half-turn can correspond to a major (wide) groove separation, designated by 'W', or an extra minor (narrow) groove separation, designated by 'N'. The strands are drawn as zig-zag helical structures, where two consecutive, perpendicular lines correspond to a full helical turn for a strand. The arrowheads at the ends of the strands designate their 3' ends. The structures contain implicit symmetry, which is indicated by the conventional markings, a lens-shaped figure (DAE) indicating a potential dyad perpendicular to the plane of the page, and arrows indicating a twofold axis lying in the plane of the page. Note that the dyad in DAE is only approximate, because the central strand contains a nick, which destroys the symmetry. The strands have been drawn with pens of two different colors (three for DAE), as an aid to visualizing the symmetry. In the case of the parallel strands, the red strands are related to the other red strands by the twofold axes vertical on the page; similarly, the blue strands are symmetrically related to the blue strands. The twofold axis perpendicular to the page (DAE) relates the two red helical strands to each other, and the two blue outer crossover strands to each other. The 5' end of the central green double crossover strand is related to the 3' end by the same dyad element. A different convention is used with DAO. Here, the blue strands are related to the red strands by the dyad axis lying horizontal on the page. An attempt has been made to portray the differences between the major and minor grooves. Note the differences between the central portions of DPOW and DPON. Also note that the symmetry brings symmetrically related portions of backbones into apposition along the center lines in parallel molecules, in these projections. The same contacts are seen to be skewed in projection for the antiparallel molecules.
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