Holliday junction

A Holliday junction is a four-way DNA branch in which strands exchange pairing partners between homologous duplexes. It can occur as an intermediate in homologous recombination. The molecular configuration is distinct from a final chromosomal crossover, which is classified by the exchange of flanking chromosome arms. Robin Holliday's 1964 model connected strand exchange, hybrid DNA and gene conversion.^[ref]

For a schematic example, label homologous regions by distant markers $L\cdots R$ and $l\cdots r$. Alternative strand-pair cleavage and rejoining routes at a junction can preserve the parental combinations $L\cdots R$, $l\cdots r$, or produce the exchanged combinations $L\cdots r$, $l\cdots R$. Local mismatches and their repair can change an allele independently of that distant-marker outcome. The historical diagram illustrates possibilities; it does not establish equal frequencies for these outcomes in every cell.^[ref]

Later work sought physical evidence. H. Potter and D. Dressler isolated colicinE1 plasmid DNA, linearized it with the restriction enzyme EcoRI, and examined it by electron microscopy. They found crossed structures containing two genome lengths, joined at homologous regions. Such forms occurred in wild-type and tested RecB-C hosts but were absent in their recombination-deficient RecA hosts. They interpreted these controlled observations as intermediates of the Holliday model.^[ref]

The combination of shape, DNA content and a genetic control is stronger evidence than an X-shaped image alone. A Holliday junction also need not be an obligatory step in every noncrossover recombination pathway; the outcome and the route producing it remain separate questions.

Branch migration is movement of the strand-exchange point in a Holliday junction. Successive changes in base pairing shift the junction along homologous DNA without requiring a new break in each phosphodiester backbone. Moving the boundary changes the extent of heteroduplex DNA, where strands from different parental DNA molecules pair together.

An illuminating experiment built two double-stranded DNA substrates with complementary single-stranded tails. Pairing the tails formed a four-stranded junction at one end. Complete branch migration to the opposite end produced two strand-exchanged duplex products, giving an observable endpoint for a process otherwise occurring along a molecular junction.^[ref]

The spontaneous reaction depended strongly on the surrounding ions: under the reported conditions, removing magnesium made it roughly a thousand times faster. This is not a universal speed for DNA exchange inside a cell; the experiment isolated a spontaneous process whose kinetics depend on junction structure and solution conditions.^[ref]