B

top duplex single-stranded breaks in each duplex strand invasion branch migration top duplex single-stranded breaks in each duplex

— hybrid duplexes

FIGURE 10-1 Holliday model through the steps of branch migration. The small arrowheads on the DMA single strands point in the 5' to 3' direction Note that A and a, B and b, C and c specify different alleles, and have slightly different DMA sequences Therefore, heteroduplex DNA containing those genes (shewn m the expanded section in panel d) will have some mismatches.

— hybrid duplexes

FIGURE 10-1 Holliday model through the steps of branch migration. The small arrowheads on the DMA single strands point in the 5' to 3' direction Note that A and a, B and b, C and c specify different alleles, and have slightly different DMA sequences Therefore, heteroduplex DNA containing those genes (shewn m the expanded section in panel d) will have some mismatches.

When illustrating the Holiday model, it is useful to picture the two homologous, double-stranded DNA molecules, aligned, as shown in Figure lU-la. These molecules, although nearly identical, carry different alleles of the same gene (as is denoted by the Ala, Bib, and C/c symbols in Figure 1U-1). which are helpful for following the outcome of recombination,

Recombination is initiated by the introduction of a nick in each DNA molecule at an identical location (Figure 10-lb), DNA strands near the nick site can then be "peeled" away from their complementary strands, freeing these strands to invade, and ultimately base-pair with, the homologous duplex (Figure iU-lc). in the structure shown in the figure, this invasion is symmetrical: thai is, the same region of DNA sequence is "swapped" between the two molecules. Strand invasion generates the Holliday junction, the key recombination intermediate,

The Holliday junction generated by strand invasion can then move along the DNA by branch migration. This migration increases the length of the DNA exchanged. If the two DNA molecules are not identical — but, for example, carry a few small sequence differences, as is true often between two alleles of the same gene—branch migration through these regions of sequence difference generates DNA duplexes carrying one or a few sequence mismatches (see Band fa alleles in Figure 10-1 d and the inset). Such regions are called heteroduplex DNA. Repair of these mismatches can have important genetic consequences, a point we return to at the end of the chapter.

Finishing recombination requires resolution of the Holliday junction by cutting the DNA strands near the site of the cross. Resolution occurs in one of two ways, and. therefore, gives rise to two distincl classes of DNA products, as we now describe.

Figure 10-2 illustrates where the alternative pairs of DNA cut sites occur on the branched DNA. To make these cut sites easier to visualize, the Holliday junction is "rotated" to give a square-planner structure with no crossing strands. The two strands writh the same sequence and polarity must be cleaved; the two alternative choices for cleavage sites are marked 1 and 2 in Figure 10-2,

The cut sites marked 1 occur in the two DNA strands that were not broken during the initiation reaction (Figure 10-lb). If these strands are now cut, and then covalently joined (the second reaction catalyzed by DNA ligase as we discuss below), the resulting DNA molecules will have the structure and sequence shown on the left in lhe bottom of the figure. These products are referred to as "splice" recombination products, because the two original duplexes are now "spliced together" such that regions from the parental DNA molecules are covalently joined together by a region of hybrid duplex. As seen by following the allele markers, generation of splice products results in reassortmenl of genes that flank the site of recombination. Therefore, this type of recombinant is also called the crossover product, as, within this DNA molecule, crossing over has occurred between the A and C genes, in contrast,, the alternative pair of cut sites in the Holliday junction (marked 2 in Figure 10-2) is in the two DNA strands thai were broken to initiate recombination. After resolution and covalent joining of the strands at these sites, the resulting DNA molecules contain a region or "patch" of hybrid DNA. These molecules are thus known as the patch products, hi these products, recombination does not result in reassortment of the genes flanking the site of initial cleavage

"splice" or crossover products "patch" cr non-crossover products reassortment of flanking genes no reassortment

"splice" or crossover products "patch" cr non-crossover products reassortment of flanking genes no reassortment

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