Holliday junction
A Holliday junction is a mobile junction between four strands of DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

. The structure is named after Robin Holliday
Robin Holliday
Robin Holliday PhD, FRS, FAA is a British molecular biologist. Heproposed a mechanism of DNA-strand exchange that attempted to explain gene-conversion events that occur during meiosis in fungi. That model first proposed in 1964 and is now known as the Holliday Junction.-Education and...

, who proposed it in 1964 to account for a particular type of exchange of genetic information he observed in yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...

 known as homologous recombination
Homologous recombination
Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks...

. Holliday junctions are highly conserved
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...

 structures, from prokaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

s to mammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...


Because these junctions are between homologous sequences, they can slide up and down the DNA. In bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

, this sliding (or branch migration
Branch migration
Branch migration describes the ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous. This usually happens when two homologous double strands form a Holliday junction and the whole structure...

) is facilitated by the RuvABC
RuvABC is a complex of three proteins that mediate branch migration and resolve the Holliday junction created during homologous recombination in bacteria. As such, RuvABC is critical to bacterial DNA repair....

 complex or RecG protein, molecular motors that use the energy of ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...

 hydrolysis to push the junction around. The junction must then be resolved, split up, to restore 2 linear duplexes. This can be done to either restore the parental configuration or to establish a crossed over configuration. Resolution can occur in either a horizontal or vertical fashion during homologous recombination, giving patch products (if in same orientation during double strand break repair) or splice products (if in different orientations during double strand break repair).

Holliday junctions are an intermediate in genetic recombination which are also of importance in maintaining genomic integrity.


In prophase of meiosis I, duplicated homologous chromosomes pair and align end-to-end. Crossover can occur between aligned chromatids, leading to exchange of homologous segments by homologous recombination.

Chromosome segregation through meiotic divisions leads to novel genotypes, first in gametes, then in offspring.

In the original Holliday model for homologous recombination, single-strand breaks occur at the same point on one strand of each parental DNA. Free ends of each broken strand then migrate across to the other DNA helix, where the invading strands are joined to the free ends they encounter. The resulting crossover junction is called a Holliday junction.

As each crossover strand reanneals to its original partner strand it displaces the original complementary strand ahead of it, causing the Holliday junction to migrate. This creates heteroduplex DNA segments
A heteroduplex is a double-stranded molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms....


Cleavage and rejoining to re-establish two separate DNAs occurs in two ways. This is most easily visualized by first rearranging the Holliday structure. DNA molecules with this apparent structure have been observed.

This structure can be resolved by cleavage in the horizontal plane, leading to two molecules that do not show crossover of markers in genes A and B.

If, instead, the same structure is cleaved in the vertical plane, both of the resulting recombinant molecules show crossover of markers in genes A and B. All products, regardless of cleavage plane, are heteroduplexes in the region of Holliday junction migration.

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