Homologous
Recombination
The most straightforward way to accomplish recombination is to break and rejoin DNA molecules, a process called homologous recombination. In 1964 Robin Holliday proposed a model (detailed in Figure 25.20) for homologous recombination between duplex DNA molecules.
Holliday proposed that recombination proceeds as follows (with steps numbered according to Figure 25.20):
1. Nicking at the same site on two paired chromosomes;
2. Partial unwinding of the duplexes is followed by strand invasion, in which a free single-strand end from one duplex pairs with its unbroken complementary strand in the other duplex, and vice versa;
3. Enzymatic ligation generates a crossed-strand intermediate, called a Holliday junction;
4. The crossed-strand structure can move in either direction by duplex unwinding and rewinding;
5. The Holliday junction "resolves" itself into two unbroken duplexes, by a process of strand breaking and rejoining. The process leading to recombination begins with isomerization of the Holliday structure (step 5), followed by strand breakage;
6 - 8 . If the original crossed strands (those that were broken in step 1) break and rejoin, the products are nonrecombinant duplexes, each containing a heteroduplex region (that is, nonrecombinant with respect to the outside markers A and Z); and
9 - 11. If the strands that will break are those that were not broken in step 1, resolution of the resulting structure generates two chromosomes recombinant for DNA flanking the region and each containing a heteroduplex region.
A modification of the Holliday model, proposed by Meselson and Radding, is shown in Figure 25.22. In it,
1. Strand displacement synthesis occurs;
2. A displaced single-strand end of the nicked duplex, A, invades the homologous region of the unbroken duplex, B;
3. The displaced loop on duplex B is cleaved and partially degraded;
4. The displaced end from duplex A is ligated to B; and
5. Isomerization then occurs, as in the Holliday model, with the originally unbroken strands crossed.
An additional feature of the Meselson - Radding model is branch migration, a process of simultaneous strand unwinding and rewinding of both duplexes, which allows the site at which the strands cross to move. As a result, the final cuts of these strands may occur some distance from the site of either strand invasion or the original nick (steps 6 and 7). In principle either a 5' or a 3' end could initiate the strand invasion process, but a 3' end probably initiates recombination in E. coli.
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