The Formation and Resolution of the Holliday Structure in Genetic Recombination

The process is shown proceeding from the left to the right. Each of the possible stages is labeled with capital or small Roman numerals. In the first stage, I, two homologous double helices (red-orange and green-cyan) of DNA align with each other. The two strands of each duplex are indicated by the two pairs of lines terminated by half arrows, which indicate the 3' ends of the strands. Each of these two homologous regions carries a flanking marker, A and B in the strands on the left, and a and b on the right. After the first step, the homologous pairs have formed a Holliday intermediate, II, by exchanging strands. Note that the two crossover strands are composite strands with both a green and an orange portion formed through any of a number of possibilities. The parallel representation of the Holliday junction is shown. The homologous twofold sequence symmetry of this structure permits it to undergo the iterative isomerization process, branch migration; movement in the direction indicated results in structure III. The Holliday intermediate may or may not undergo the crossover isomerization process to produce structure IV, in which the crossover and non-crossover strands are switched. Note that this process only has meaning if the Holliday intermediate is two-fold symmetric, rather than fourfold symmetric. Although indicated as separate, the crossover isomerization process could be a feature of branch migration. If crossover isomerization occurs an odd number of times, resolution by cleavage of the crossover strands yields structure V, but structure v results if crossover isomerization occurs an even number of times (including 0) before cleavage. Ligation of v generates a patch recombinant, vi; this is a pair of linear duplex DNA molecules containing heteroduplex DNA because of branch migration, but which have retained the same flanking markers. Ligation of VI yields splice recombinant molecules, that have exchanged flanking markers.

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