DNA repair

Each of us has around 10^13 cells in our body, a mutation in just one of these can lead to a cancer. Thus it is crucially important that each cell has an advanced system for the detection of DNA damage and the control of appropriate response measures. These may be repair, via a number of pathways dependent on the type of damage, or senescence or even apoptosis when damage is severe.

Extent of damage

As many as one million lesions may occur per day in a single human cell. Damage can occur from endogenous sources, such as reactive oxygen species produced by metabolism. But it also created exogenously, by ultraviolet light and other ionising radiation, mutagens and viruses.

These can cause

  1. Oxidation of bases
  2. Alkylation of bases
  3. Hydrolysis – e.g. deamination, depurination, depyrimidation
  4. Formation of ‘bulky adducts’
  5. Mismatched bases

Every time a cell undergoes division its telomeres shorten. When these reach the Hayflick limit, the cell goes into senescence, an irreversible dormant state.

DNA repair

Direct reversal

  • Pyrimidine dimers, which are formed by UV irradiation, are repaired by photolyase on its activation by UV (photoreactivation).
  • Guanine methylation is reversed by methyl guanine methyl transferase
  • Some C and A methylation can also be directly reversed
  • The adaptive response in E.coli, upon alkylation of DNA backbone. Ada suicidally transfers alkyl groups onto its cysteine residues (not catalysis, stoichiometric). Methylation of ada -> activation of itself, + other alkylation responsive genes.

Single strand damage

  • Base-excision repair (BER) after oxidation, alkylation, hydrolysis or deamination
    Damaged base is removed by DNA glycosylase
    AP endonuclease recognises “missing tooth” and cuts phosphodiester bond, allowing resynthesis by DNA polymerase. Then ligase seals backbone.
  • Nucleotide excision repair (NER) recognises bulky lesion s which distort the helix (e.g. thymine dimers). Requires Uvr system in E. coli, = UvrABC + DNA Helicase II. UvrA-UvrB scans DNA, UvrA recognises distortions, leaves complex to be replaced by UvrC. UvrB cleaves bond downstream of DNA damage while UvrC cleaves upstream. Helicase II breaks hydrogen bonds to remove excised segment. The gap is filled by DNA Pol I.
  • DNA mismatch repair (MMR) is strand-specific, the daughter strand is recognised as the one to be corrected. Three proteins are involved mutS, mutH and mutL. mutS forms a dimer that recognises the daughter strand’s mismatched base and binds, mutS recruits mutL dimers. MutH binds to hemimethylated sites, and is activated by mutL. It nicks the daughter strand and recruits DNA helicase II. MutSHL then travels behind the helix along the single strand it creates towards the mismatch. An exonuclease digests the tail left behind. The process ends past the mismathed site and PolIII can then repair the daughter strand.

Double strand breaks

  • NHEJ – DNA Ligase IV uses microhomology to rejoin two ends (also used in VDJ recombination. Ku?
  • Micro-homology mediated end joining (MMEJ) uses the Ku protein too
  • Homologous recombination-uses sister chromatid/ homolgous chromosome

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