DNA Repair Mechanisms Notes

DNA repair systems are crucial for cellular survival due to the harmful nature of most mutations.
Cells have multiple repair mechanisms targeting various types of DNA damage, typically involving three main steps:
- Detection of irregularity in DNA structure.
- Removal of the abnormal DNA segment.
- Synthesis of new, normal DNA to replace the removed segment.

Some damages can be directly repaired:
- Photolyase repairs thymine dimers by splitting the dimers using visible light energy, restoring the original DNA structure.
- Alkyltransferase repairs alkylated bases by transferring the alkyl group from the base to a cysteine side chain on the enzyme, resulting in irreversible inactivation of alkyltransferase.

Thymine Dimer Repair: Photolyase cleaves the bonds between thymine dimers, restoring DNA structure.
- Reaction:
  1. Cleavage of thymine dimer bonds.
  2. Restoration of normal thymine structure.
6-Methylguanine Repair: Alkyltransferase transfers the methyl group from guanine to itself, restoring normal guanine structure.

Base Excision Repair (BER) is a process that removes damaged bases using enzymes called DNA N-glycosylases.
Enzymes recognize abnormal bases (like uracil or 3-methyladenine) and cleave the bond between the base and the DNA sugar.
The specific steps include:
- Cleavage of the damaged base to create an apyrimidinic site.
- AP endonuclease recognizes the missing base.
- DNA polymerase replaces the missing base and ligases seal the break in both prokaryotes and eukaryotes.

Nucleotide Excision Repair targets a broad range of DNA damages, including thymine dimers, missing bases, and chemically modified bases.
NER involves:
- Recognition of the damaged segment by a protein complex (e.g., UvrA, UvrB, UvrC in E. coli).
- Removal of a short segment of the damaged DNA.
- DNA polymerase reconstructing the damaged section.
- Example: Xeroderma pigmentosum is linked to defects in the NER genes.

UvrA/UvrB complex tracks DNA.
Upon damage detection, UvrA is released; UvrC binds, creating cuts on both sides of the damage.
UvrD helicase removes the damaged DNA segment.
DNA polymerase fills the gap, followed by ligase sealing the repair.

Mismatch Repair Systems correct base pair mismatches in DNA, which may occur during DNA replication.
MMR is critical for maintaining the integrity of the DNA and involves:
- Recognition of mismatches by proteins (MutS, MutL, MutH in E. coli).
- MutH distinguishes the parent strand (methylated) from the daughter strand (not methylated).

MutS detects mismatched base pairs.
The MutS/MutL complex assists MutH to bind at hemimethylated sites.
The mismatch is excised and replaced with the correct nucleotide by DNA polymerase.

Double-Strand Breaks (DSBs) are critical injuries that can lead to severe chromosomal damage.
Two primary repair mechanisms:
- Homologous Recombination Repair (HRR): Utilizes sister chromatids as templates for accurate repair during S and G2 phases.
  - Steps include strand invasion and synthesis using the unbroken strand as a template.
- Non-Homologous End Joining (NHEJ): Repairs breaks without needing a template, can occur at any cell cycle stage, but may introduce deletions and is error-prone.

Translesion DNA Polymerases allow replication past lesions that escape repair mechanisms.
These specialized polymerases have a flexible active site enabling them to accommodate distorted DNA structures, albeit with a higher rate of errors compared to replicative polymerases (mutation rates between $10^{-2}$ to $10^{-3}$ ).

Involves crossing over of homologous DNA segments and plays a role in meiosis and genetic diversity.
Gene conversion can result from homologous recombination by aligning sequences closely and repairing mismatched bases.

RecBCD complex recognizes double-strand breaks.
RecA promotes strand invasion.
RuvAB/C involved in branch migration and resolution of Holliday junctions for chromosomal separation.

Gene conversion is a process by which homologous recombination results in identical alleles from different alleles, occurring primarily through mismatch repair or gap repair synthesis.