The Holliday Model

One model of homologous recombination, the Holliday junction, states that the process is initiated by singlestrand breaks in the DNA molecule. This model begins with double-stranded DNA molecules from two homologous chromosomes that carry identical (or nearly identical) nucleotide sequences. These two DNA molecules align precisely, and so their homologous sequences sit side by side (IFigure 12.23a). Single-strand breaks in the same position on both DNA molecules allow the free ends of the strands to move to the other DNA molecule (iFigure 12.23b and c). Each invading strand joins to the broken end of the other homologous DNA molecule and begins to displace the original complementary strand, taking its place by hydrogen bonding to the original strand. The invasion and joining take place on both DNA molecules, creating two heteroduplex DNAs, each consisting of one original strand plus one new strand from the other DNA molecule. The point at which nucleotide strands pass from one DNA molecule to the other is the cross bridge. In the Holliday model of recombination, there is a single cross bridge. As the two nucleotide strands exchange positions, the cross bridge moves along the molecules in a process called branch migration (IFigure 12.23d). The exchange of nucleotide strands and branch migration create two duplex molecules connected by the cross bridge. This structure is termed the Holliday intermediate. Holliday intermediates in E. coli and yeast have been observed with electron microscopy.

If the ends of the two interconnected duplexes illustrated in Figure 12.23d are pulled away from one another, we obtain the structure illustrated in 4 Figure 12.23e. If you carefully compare parts d and e, you will see that the structures in each are the same; the only difference is that, in part e, the ends of the molecules have been pulled apart.

The next step in the Holliday model is easier to visualize if we rotate the bottom half of the Holliday intermediate by 180 degrees, producing the structure shown in 4 Figure 12.23f. These interconnected DNA duplexes are then separated by additional cleavage and reunion of the nucleotide strands. The duplexes can be cleaved in one of two ways, as shown by two different pathways in Figure 12.23. Cleavage may be in the horizontal plane (iFigure 12.23g), in which case the nucleotide strands are rejoined as shown in 4 Figure 12.23h, and two DNA molecules are produced. Although both resulting DNA molecules contain a patch of heteroduplex DNA, the genes on either end of the molecules are identical with those originally present (gene A with B, and gene a with b). These DNA molecules are called patched recombinants (i Figure 12.23i).

On the other hand, cleavage of the Holliday structure in the vertical plane and rejoining of the nucleotide strands (I Figure 12.23j) produces spliced recombinants (I Figure 12.23k). In these recombinants, both resulting DNA molecules are heteroduplex, and recombination has taken place between loci at the ends of the molecules; now gene A is paired with b, and gene a is paired with B. Recombination is equally likely to produce patched and spliced recombinants. An animated cartoon that will help you visualize the Holliday structure and its resolution

^ Branch migration takes place as the two nucleotide strands exchange positions, creating the two duplex molecules.

Heteroduplex DNA

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