Holliday structure, the most important intermediate in recombination is also known as Holliday junction or half chiasma. The first molecular model of the genetic exchange that occurs between homologous chromosomes during recombination was proposed by Robert Holliday. This Holliday model involves several steps.
First the homologous chromosomes are both nicked at identical location. Then the strands from one side of the nicks invade the homologous chromosomes, base pairing with no complementary strands. The invading strands are next covalently linked to the original strands at the nick site, forming what is called a Holliday junction. The Holliday junction migrates away from the original nick site, a process called branch migration. As it does so, the DNA strands are swapped between the chromosomes. This creates heteroduplex regions on both chromosomes, where man made or bases sequence differences between homologous chromosomes result in a region of DNA with a low percentage of mismatched base pairs.
The length of branch migration may vary, but some point breaks are made in the DNA that end migration and resolves the entangled DNA strands into two separate chromosomes. There are two ways that breaks can be made; one results in recombinant chromosomes.
If the crossed strands are cleaved by endonucleases, the after ligation within the chromosomes there will be two the chromosomes there will be two non recombinant chromosome with short heteroduplex regions. Alternatively if one rotates on DNA helix 180 0, a process called isomerisation, we can visualise how un crossed strands can be broken. After the uncrossed strands are cleaved by an endonucleases, ligation can produce recombinant chromosomes with short heteroduplex regions