DNA Replication and Repair Mechanisms

DNA Replication and Repair Mechanisms

• DNA damage is common and detrimental, especially during replication. Damage impacts replication in various ways.

Outcomes of Lesions During Replication

• Translesion Synthesis (TLS): DNA synthesis continues over the lesion using specialized DNA polymerases. This is often the case with a lesion that doesn't significantly distort the DNA. A common result of TLS is a mutation.
• Lesion Repair and Fork Collapses: If repair is initiated but incomplete when the replication fork arrives, the fork collapses, creating a double-strand break (DSB). Recombinational repair fixes this.
• Replication Fork Stalling: Replisome halts at the lesion. Replication can restart downstream, leaving the lesion behind. The lesion is in a single-stranded gap. This is more common in delaying strand..
• Replication Bypass and Restart: The replication machinery halts but picks up again. The lesion is left behind, in a single-stranded gap. This bypass is more common on the lagging strand due to how Okazaki fragments are generated.

DNA Double-Strand Break Repair (DSBR)

• Double-strand breaks (DSBs) are lethal if not repaired. They can originate from oxidative damage or radiation.
• DSBR utilizes homologous recombination; requires an undamaged homologous DNA molecule, for example, a sister chromatid.
• DSBR Pathway:
  • Broken DNA ends are processed.
  • The 3’ strands invade the homologous chromosome.
  • The invading strand is replicated.
  • The invading strand is used for replication to restore the damaged piece of DNA using the homologous chromosome as a template.
• Repair pathways utilize recombination.
  • The DNA double crossover intermediate has multiple resolution options.
    • Synthesis-Dependent Strand Annealing (SDSA): The invading strands are displaced, and any gaps are filled.
    • Double-Strand Break Repair (DSBR): The strands are linked until replication is completed, forming a Holliday intermediate. Holliday Junction Resolvases cleaves the Holliday intermediate in ways that retain or exchange the chromosomal DNA segments.

Replication Fork Repair

• Collapsed Replication Forks: A broken template strand leads to a DSB. Recombinational repair recreates the replication fork. The steps are similar to DSBR.
  • Broken DNA end is processed to create a single-stranded extension.
  • The strand then invades the intact chromosome.
  • Branch migration moves the branch point in one direction, usually.
  • The branch can be resolved, and replication can restart without mutations..
• Stalled Replication Forks: The fork stops at the lesion. This triggers fork regression (fork moves backward) to bring the lesion into contact with its complementary strand. It results in a four-branched Holliday intermediate. It also allows further repair. This lesion can be repaired by DNA excision repair or other relevant pathways..

Gap Repair

• A lesion can cause single-stranded gap in which TLS fills in the missing DNA segment. If TLS is mutagenic, recombinational gap repair happens in another way.
• Gap Repair Pathway:
  • A recombinase binds to the single-stranded gap.
  • Recombinase promotes strand invasion into the undamaged double-stranded DNA of the replication fork.
  • Branch migration generates Holliday intermediates.
  • The displaced strand acts as a template allowing further DNA replication.
• The Holliday intermediates are resolved, resulting in non-crossover pathways, and gaps are filled. NER, BER can begin at the lesion.