Holliday junction immobile

Double-crossover molecules have been used extensively to characterize the properties of Holliday junctions. The strong torsional coupling between their crossover points has been exploited to construct symmetric immobile junctions (S. Zhang et al. 1993), junctions in which one of the crossovers is flanked by homology, but is nevertheless unable to branch migrate. Symmetric immobile junctions have been used to characterize crossover isomerization thermodynamics (S. Zhang and Seeman 1994) and, more recently, the sequence dependence of the branch point stability (W. Sun et al., 1998). Double crossover molecules have also been employed to establish the cleavage patterns of endonuclease VII, an enzyme that resolves branched junctions (Fu et al. 1994 a). 

The Holliday junctions formed during recombination are mobile, but synthetic immobile Holliday junctions can be synthesized by using nonhomolo-gous base sequences or by locking the jrmctions. This has permitted careful physical study of these and other more elaborate synthetic junchons. With suitable choices of base sequences for the oligonucleotides from which they are made, such junctions will assemble spontaneously. Double-stranded DNA with immobile junctions is a very suitable construction material on a "nanochemical" scale. It has been assembled into knots, rings, cubes, and more complex polyhedra. ... 

Figure 16 Branched DMAs as building blocks for DNA self-assembly, (a) A Holliday junction and its branch migration (b) an example of immobile junctions (c) formation of an ideal two-dimensional lattice from an immobile junction (d) formation of a cyclic complex from eight immobile junctions due to variable angles between the arms. (Adapted from N.C. Seeman. Angew. Chem. Inti. Ed. 37 3220-3238, 1998, and N.C. Seeman. Biochemistry 42 7259-7269, 2003. With permission.)...

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