intro to dna damage repair

Point Mutations:
- Caused by improper base pairing during DNA replication.
- Types:
- Transition: Purine ↔ Purine (A ↔ G), Pyrimidine ↔ Pyrimidine (C ↔ T)
- Transversion: Purine ↔ Pyrimidine (A or G ↔ C or T)
Insertions or Deletions: Alterations leading to changes in the DNA sequence.

Cells possess mechanisms to repair DNA damage using the undamaged strand as a template.
Errors may escape repair, leading to mutations in daughter DNA strands.

Accumulation of mutations, especially in eukaryotic cells, is linked to cancer development.
- Thousands of errors occur daily; only 1 in 1000 can become a mutation due to robust DNA repair systems.
Over 130 DNA repair proteins are present in the human genome.

DNA damage can be severe, including:
- Breaks in the DNA backbone (single-strand vs. double-strand breaks).
- Loss of entire chromosomes or portions thereof.

Exogenous Factors:
- UV Light: Can cause thymine dimers.
- X-rays/Ionizing Radiation: Cause double-strand breaks.
- Chemical Exposure: From environmental sources leads to base modifications.
- Oxygen Radicals: Result from metabolic processes causing oxidation of bases.
Endogenous Factors:
- Radiation from sources like gamma rays.
- Viral infections impacting DNA.
- Some chemotherapeutic agents.

Arise due to base mismatching (e.g., A binding with G instead of T).
- Involves water acting as a mediator.
Rare amino tautomers can mispair (e.g., adenine pairing with cytosine).

Methylation:
- In E. Coli, the parent strand is methylated by dam methylase, which adds CH₃ groups on adenines within the GATC sequence.
- Only the parent strand remains methylated after replication; daughter strands lack this methylation.
Mismatched Base Pair Recognition:
- Proteins Muts and MutL bind to mismatched pairs and recognize them using ATP hydrolysis.
MutH Functionality:
- Binds to MutL and hemimethylated GATC sequences.
- Cleaves the unmethylated strand to initiate repair.
DNA is unwound; exonucleases and helicase work to degrade non-methylated DNA to the mismatch.
DNA Polymerase III and DNA ligase replace and seal the missing sequence.

Muts and MutL are conserved across bacteria, while MutH is more specific.
Eukaryotes have homologous proteins, but details of mismatch repair mechanisms vary and are less understood than in prokaryotes.

Involves specific DNA glycosylases removing damaged or modified bases (e.g., uracil glycosylase).
Uracil Glycosylase:
- Targets uracil (produced from cytosine deamination) which should not be present in DNA.
Cleaves the glycosidic bond without damaging the backbone leaving an abasic site.
Recognized by an AP endonuclease to cleave the backbone near the lesion.
New DNA is synthesized by DNA polymerase I, followed by ligation from DNA ligase.

Targets large lesions/distortions from agents like UV light.
In E. Coli, proteins with exonuclease activity (UVRA, UVRB, UVRC) bind to the site, cleaving the DNA around the lesion.
The gap left is filled by polymerases and sealed by ligase.

Photolyases utilize light energy to repair pyrimidine dimers.
- Not present in humans or placental mammals.
O⁶ Methylguanine DNA Methyltransferase:
- Repairs methylation on guanine molecules, reversing mispairing potential with thymine.
ALKB:
- Repairs methylated adenines and cytosines through oxidative demethylation.

Useful for single and double-stranded breaks.
Homologous Recombination:
- An exchange between similar DNA sequences re-establishes continuity in a broken strand.
Nicks lead to single-stranded extensions, which pair with complementary strands to create Holliday intermediates, cleaved and ligated to restore replication.

SOS Response in E. Coli:
- Initiated in response to extreme DNA damage.
- Can include exonucleases and specialized DNA polymerases (DNA pol V).
- Allows bypassing of lesions but leads to high mutation rates.

Extensive variety of DNA damage leads to mutations, potential cancer, and cell death.
DNA repair mechanisms are critical in maintaining genomic integrity and preventing the transmission of mutations.