Mechanisms of DNA Repair

Introduction to DNA Repair Mechanisms

  • The video discusses mechanisms of DNA repair.

  • Purpose: To explain how cells recognize and repair DNA damage, matching repair mechanisms to specific types of damage.

Overview of DNA Damage Repair Mechanisms

  • Errors or damage in DNA are repaired by various mechanisms depending on the timing and extent of the damage.

  • All repair pathways generally follow the same steps:

    • Step 1: Remove the damaged DNA section by cutting the phosphodiester bonds.

    • Step 2: Repair the damage (usually requiring a polymerase).

    • Step 3: Seal the gaps using a ligase.

Key Enzymes in DNA Repair

  • The primary enzymes involved in the repair steps are:

    • Nuclease: Cuts DNA.

    • Polymerase: Repairs damage.

    • Ligase: Seals the DNA strands.

DNA Polymerase Functions

  • DNA polymerases have three enzymatic functions:

    • Polymerase Activity: Synthesizes DNA from 5' to 3'.

    • 5' to 3' Exonuclease Activity: Removes RNA primers.

    • 3' to 5' Nuclease Activity: Fixes DNA mismatches.

Mechanism of Mismatch Detection and Repair

  • DNA polymerase can make mistakes due to a guess and check mechanism based on binding affinity:

    • If a mismatch occurs at the 3' end of the newly synthesized strand, the damaged segment is flipped into the nuclease site of DNA polymerase.

    • The exonuclease activity chews back the incorrect DNA, allowing the polymerase to continue synthesizing the correct strand.

Mismatch Repair Mechanism

  • Mismatch repair must occur before cell division while DNA is differentially methylated, aiding in strand identification:

    • Methylation occurs on specific nucleotides (adenine in bacteria, cytosine in eukaryotes).

    • The parent strand is recognized due to its methylation status, allowing the cell to distinguish between the parent and daughter strands.

  • Steps of mismatch repair:

    • Identify the mismatch on the unmethylated daughter strand.

    • Cut out the damaged section, replace it with the appropriate nucleotide using polymerase, and use ligase to seal the strand.

Base Excision Repair (BER)

  • BER repairs damage that can happen in interphase (G1 and G2) due to mismatches or chemical damage:

    • Occurs during checkpoints where the cell assesses DNA integrity before replication or mitosis.

    • Steps in Base Excision Repair:

    • Remove the damaged base but not the entire nucleotide to avoid breaking phosphodiester bonds.

    • Trigger the removal of the entire nucleotide (cutting phosphodiester bond).

    • Repair the gap with DNA polymerase and ligate the DNA strands.

Nucleotide Excision Repair (NER)

  • Repairs lesions such as thymidine dimers, which result from adjacent thymines becoming covalently linked:

    • NER must remove both cross-linked nucleotides:

    • The cut encompasses a whole turn of the helix (about 10 nucleotides).

    • Following excision, DNA polymerase synthesizes a new strand using the complementary strand as a template, and ligase seals the repaired piece back to the original strand.

Double Strand Break (DSB) Repair Mechanisms

  • DSBs are repaired differently due to the complexity of the damage:

    • Two main mechanisms:

    • Non-Homologous End Joining (NHEJ): A simple ligation approach where broken ends are trimmed and then joined together by a ligase.

      • This can cause genomic rearrangements and translocations if ends are improperly paired leading to disrupted regulatory networks.

    • Recombination: More complex and involves additional mechanisms (not covered in this video).

Implications of DNA Repair Mechanisms

  • These mechanisms significantly improve genomic integrity, reducing the error rate from approximately 1 in 10,000 base pairs to about 1 in a trillion base pairs.

  • With a genome size of roughly 3.6 billion base pairs, such mechanisms ensure near error-free replication of the entire genome.