Homologous Recombination

An essential requirement of DNA replication is to maintain the integrity of the genetic material. For this reason double-strand breaks are preferentially repaired by homologous recombination and it is typically carried out after DNA synthesis when the two daughter DNA molecules are in proximity, and one can serve as a template for repair of the other.

In eukaryotes, a protein complex called MRN, composed of specialized nucleases degrade the damaged ends of the DNA while ends tethered to each other. The DNA is left with single-strand overhangs of 3-4 nucleotides with a 3’ OH end. This single-stranded section is stabilized by RPA proteins until Rad51 - homolog of prokaryotic protein RecA - is activated by ATP, and binds to the DNA forming a filament.

In the filament, the DNA exists as triplets of nucleotides where the DNA backbone is unwound between adjacent triplets. This DNA-protein filament binds to a duplex DNA from a sister chromatid by stretching the intact template DNA and destabilizing it, so that the two strands can be easily pulled apart and the broken strand can attempt to bind to the template, in a process known as strand invasion.

The invading strand searches for undamaged, homologous sequences in the genomic DNA by trying to form base pairs in a block of three nucleotides. If the basepairs mismatch, the invading DNA dissociates and looks for other homologous regions. If one triplet from the invading strand matches with the template, then the next three nucleotides are sampled. 

If a sequence matches for a stretch of at least five triplets, a displacement loop structure is formed, with DNA polymerase using the invaded strand as a template.

Following this, a helicase displaces the now extended invading strand which basepairs with the uncoated damaged strand. Next, the second damaged strand anneals to the complementary strand of the template DNA for another round of DNA synthesis. Finally, the sister strands dissociate and a DNA ligase seals the nicks, restoring the repaired helices, and ensuring accurate repair of the intact chromosome.