Holliday junction

-First, the homologous chromosomes are both nicked at identical locations.

-Then, the strand from on side of the nicks invade and base-pairs with the other homologous complementary strand.

-The invading strand is covalently linked to the original strand at the nick site, forming Holiday junctions.

- The Holiday junction migrates away from the original nick sites in which this is called branch-migration.

- As it does so, the DNA strands are swapped between the chromosomes. This creates the heteroduplex regions on both chromosomes where minor base sequence differences between homologous chromosomes result a region of DNA with low percent of mismatches base-pairs.

Now, what happens if cleavage happens? To answer this, there are 2 ways that they can happen

1/
- At some point of the branch migration process,  breaks are made in the DNA that end the migration and resolves the entangles DNA into two separate chromosomes. This results both non-recombinant chromosomes and recombinant chromosomes. If cleavage takes place at the cross-strands by endonuclease, then after the ligation within chromosomes, there will be two non-recombinant chromosomes with short heteroduplex regions.

2/
- Alternatively, if one rotates one DNA helix 180o ( a process called isomerization), and if the cleavage takes place between uncross strands by endonuclease, ligation can produce recombinant chromosomes with short heteroduplex regions.