An Immobile Branched Junction
The junction shown is composed of four strands of DNA, labeled with Arabic numerals and drawn in four colors, red (1), green (2), magenta (3) and cyan (4). 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; the arms are numbered with Roman numerals. The hydrogen bonded base paring that forms the double helices is indicated by the dots between the bases. The sequence of this junction has been optimized to minimize symmetry and non-Watson-Crick base pairing. Because there is no homologous twofold sequence symmetry flanking the central branch point, this junction cannot undergo the branch migration isomerization reaction. The molecule is designed by minimizing sequence symmetry; this means that all short segments of sequences (tetramers here) are unique. At the upper part of arm I, two of the 52 unique tetrameric elements in this complex are boxed; these are C.G.C.A and G.C.A.A. At the corner of strand 1, the sequence C.T.G.A is boxed. This is one of twelve sequences in the complex (3 on each strand) that span a junction. The complements to each of these 12 sequences are not present. Whereas tetrameric elements have been used to assign the sequence of this molecule, there is redundancy in the molecule amongst trimers, such as the A.T.G sequences shown in dotted boxes.
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