Branch migration

The invading 3 end is extended by DNA polymerase plus branch migration, eventually generating a DNA molecule with two crossovers called Holliday intermediates. 

FIGURE 25-32 Branch migration. When a template strand pairs with two different complementary strands, a branch is formed at the point where the three complementary strands meet. The branch "migrates" when base pairing to one of the two complementary strands is broken and replaced with base pairing to the other complementary strand. In the absence of an enzyme to direct it, this process can move the branch spontaneously in either direction. Spontaneous branch migration is blocked wherever one of the otherwise complementary strands has a sequence nonidentical to the other strand. 

Continued branch migration yields a circular duplex with a nick and a displaced linear strand (left) or a partially single-stranded linear duplex (right). 

Once a Holliday intermediate has formed, a host of enzymes—topoisomerases, the RuvAB branch migration protein, a resolvase, other nucleases, DNA polymerase... 

DNA transposition 978 meiosis 979 branch migration 980 double-strand break repair model 980 Holliday intermediate 980... 

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... 

In step b branch migration takes place, separating the nonhomologous base pairs TA and CG and causing mismatched pairs which will be subject to repair. (B) Proposed three-dimensional structure (after drawing by Bennett and West).292... 

DNA heteroduplex extension % >CDcri 3 (Double HoUifeyJuhdloitt 5 1 3 Branch migration proteins (RuvAB and RecG)... 

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.

Figure 5-28 (A) Abbreviated reaction sequence for formation of a four-way FfoUiday junction between two homologous DNA duplexes. In step a strands are cut and rejoined with movement of the strands to a roughly antiparallel orientation. The resulting structure is thought to resemble that shown below the four-stranded representation. In step b branch migration takes place, separating the nonhomologous base pairs TA and CG and causing mismatched pairs which will be subject to repair. (B) Proposed three-dimensional structure (after drawing by Bennett and West). ...

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. 8.7, In strand-displacement assays, two regions are distinguished in an analyte (S and T ). The T reacts with the T (target C) and displaces a short signal sequence from this complex by branch migration (D). The liberated signal sequence (S ) is removed from the well (E) and detected (F).

Branch migration caused by base pairing exchange leads to the transfer of a segment of DNA from one homologue to the other. 

---