It discusses homologous recombination (HR) and non-homologous end joining (NHEJ) as the strategies cells use to repair double-strand breaks (DSBs) in DNA. Also discussed is site-specific recombination, which rearranges DNA molecules by breaking and rejoining strands at specific points.

Key aspects covered include:

• DNA Damage and Repair: Organisms are exposed to DNA-damaging agents, and if the damage isn't repaired, it can impact health. DNA repair mechanisms protect DNA.
• Double-Strand Breaks (DSBs): Considered the most toxic DNA lesion, DSBs can be caused by endogenous or exogenous factors and can lead to disease states if left unrepaired. Cells adopt strategies to repair DSBs to maintain healthy existence.
• Homologous Recombination (HR): Repairs DSBs using a sister chromatid as a template, making it a high-fidelity process. It promotes pairing between identical DNA sequences and the exchange of genetic material. HR is also involved in rescuing stalled replication forks.
• Non-Homologous End Joining (NHEJ): Repairs DSBs by rejoining broken DNA ends, regardless of the DNA sequence. This method is error-prone, and small deletions may occur at the break site.
• Alternative NHEJ (A-NHEJ): A third form of DSB repair similar to NHEJ.
• Decision-Making in DNA Repair: The cell decides which pathway to use for DSB repair based on the involvement of certain players like MRN or Ku70/80 heterodimer.
• RecBCD and RecA in Prokaryotes: In prokaryotes, RecBCD processes DNA ends resulting from DSBs. RecA protein binds to single-stranded DNA and helps in strand invasion.
• Homologous Recombination in Eukaryotes: Involves the Mre11-Rad50-Nbs (MRN) complex. BRCA1 and p53 influence the choice between homologous recombination and non-homologous end joining.
• NHEJ Pathway: Depends on Ku heterodimer and DNA-PK catalytic subunit. Ku binds to DNA ends at the DSB and improves binding by nucleases, polymerases, and ligase components.
• Alternative NHEJ (Alt-EJ/A-NHEJ): Functions on simple end-joining principles but repairs DSBs slower than conventional NHEJ. It is considered a backup pathway.
• Site-Specific Recombination: DNA molecules are rearranged by breaking and rejoining strands at specific points. It involves excision, insertion/integration, or inversion. It targets short DNA sites with well-defined sequences, and typically a single protein or a pair of proteins are involved.
• Types of Site-Specific Recombinases: Classified into tyrosine type or serine type recombinases, based on the amino acid residue mediating catalysis.
• Tyrosine Recombinases: Found in prokaryotes, archaea, and eukaryotes, sharing a catalytic domain.
• Serine Recombinases: Generally bind their individual crossover sides as dimers, but the strand exchange reaction occurs within a tetramer.
• Applications of Site-Specific Recombinases: Used in in vivo genome engineering for knock-in and knockout.