General Genetics/Molecular Evolution
When recombination is site-specific, it can only occur at specific regions of homology.
Originally called "bastard recombination," illegitimate recombinations can occur even when there is little to no homology. Transposons are capable of illegitimate recombination.
Homologous or Generalized Recombination
Holliday model of recombination
After homologous chromosomes align, a single strand of each DNA breaks and invades the other DNA. Enzymes such as ligase seal the crossed strands, and the two double-helices swap
The Holliday intermediate will be resolved in one of two ways: creation of a patched duplex or creation of a spliced duplex.
Meselson and Radding model of recombination
After homologous chromosomes align, a single strand of DNA is nicked and replicated. The replicated DNA displaces the original strand, which now dangles from the double-helix and is known as a whisker. The whisker invades the homologous double-helix and displaces that DNA, which is excised. The whisker is ligated to the new double-helix. Branch migration ensues and, from there, this model is identical to the Holliday model.
This model is supported by the discovery of Rec A and Rec BCD. Rec BCD is an E. coli protein with DNA helicase activity capable of making single-stranded nicks. This would allow it to form the "whiskers" characteristic of the Meselson-Radding model. Rec A is capable of coating exposed ssDNA and integrating it into dsDNA, which would occur during whisker invasion of the homolog in the Meselson-Radding model. E. coli is not recombination when the genes that encode Rec A and Rec BCD are knocked out.
Other proteins with potential roles in recombination
PRDM9 is a zinc finger protein. methylates lysine 4 of histone 3. In the process, it recruits enzymes that creates double-stranded DNA breaks. Since PRDM9 is polymorphic, it can promote DNA cleavage at different sites. A zinc finger is a common protein structural motif characterized by stabilization of its folds by zinc ions. Most DNA-binding proteins have the zinc finger motif.
Ruv (repair UV radiation) AB promotes branch migration. Ruv C binds to the Holliday junction and cleaves the crossover strands.