Holliday junction branch migration

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). 

An important characteristic of Holliday junctions formed from homologous duplexes is that they can move by a process called branch migration.295 Because of the twofold symmetry of the branched structure the hydrogen bonds of one base pair can be broken while those of a new base pair are formed, the branch moving as shown in Fig. 5-28. Notice that, in this example, the nonhomo-logous (boxed) base pairs TA and GC have become mispaired as TG and AC after branch migration. More significantly, the junction may be cut by a resolvase at the points marked... 

Figure 7 Repair of the double-strand break by homologous recombination in mammalian cells. In homologous recombination, an intact homologous chromosome is used to retrieve information and repair double-strand breaks in the duplex. The three basic steps of homologous recombination are strand invasion, branch migration, and Holliday junction formation.

Cre catalyzes the formation of Holliday junctions as well as their resolution. In contrast, other proteins bind to Holliday junctions that have already been formed by other processes and resolve them into separate duplexes. In many cases, these proteins also promote the process of branch migration whereby a Holliday junction is moved along the two component double helices. Branch migration can affect which segments of DNA are exchanged in a recombination process. 

Fig. 5. Two alternative models for error-free PRR via recombinational processes. (A) A strand exchange model, and (B) a template switching model. Both models propose that progression of leading strand synthesis in the presence of replicationblocking DNA damage (represented by a triangle) requires the association of the two nascent DNA strands, followed by resolution of the intermediary structure via (A) cleavage of the Holliday junction or (B) reverse branch migration. Adapted from Broomfield et al. (2001).

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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