R3.7: Basics Of DNA Repair

There are numerous repair pathways which are activated in response to DNA damage. For therapeutic radiation, the repair of double strand breaks is the most important as these seem to be the lesions that lead to cell death.

Difficulties with Double Strand Breaks

Double strand breaks (DSBs) are difficult problems for the cell to repair. The two ends may dissociate, although the histone molecules may provide some structual support. If sevearl breaks are formed in a cell, then the cell may unite the strands incorrectly. The final problem is that there may not be an appropriate template to repair the damage, particularly in G1 and early S phases.

Double Strand Break Repair

DSB repair is performed by two cellular processes: Homologous Recombination and Non-Homologous End Joining

Homologous Recombination (HR)

This is the ideal repair pathway, but it requries an undamaged copy of the DNA to function. This undamaged copy is only present after DNA replication has occured: ie, in late S phase, G2 phase and in early mitosis. This means that homologous recombination only occurs after duplication of the DNA has occured in preparation for mitosis.
The first step in HR is the detection of the double strand break. This is performed by the ATM/ATR gene products, as well as the MRN complex. When activated, these proteins signal numerous other molecules (including TP53), inducing a cell cycle arrest. The ends of the damaged DNA strand are processed and damaged bases are removed. The resulting repair process attracts the sister chromatid, unwinds it and uses the undamaged DNA strand of the sister chromatid to fill in gap left by the double strand break.
Homologous Recombination is the more accurate of the DSB repair pathways, as it uses an undamaged template to replace the damaged section.

Non-Homologous End Joining (NHEJ)

Non-homologous end joining is used in all phases of the cell cycle, as it does not require a sister chromatid to function. Each side of the double strand break is recognised by XRCC5 and XRCC6 (Ku-70 / Ku-80). These attract PRKDC to the break, which bridges the gap and notifies the cell that damage has occured through phosphorylation of numerous signalling molecules. A collection of NHEJ related proteins then processes each end before ligating the ends together.

Other DNA repair mechanisms

Radiation also induces a number of other errors in the DNA strand, which are more easily repaired.

Base Excision Repair (BER)

BER is perhaps the most straightforward of the repair pathways. It is used when a single base has been damaged. This is recognised by DNA glycosolase, which excises the base. The DNA is then 'nicked' by the AP endonuclease enzyme, leaving a single strand break.
The alternative method of arriving at this situation is when radiation induces a single strand break, which is then recognised by the PARP protein. The ends are processed to leave a 'clean' single strand break, similar to the scenario that arises from base damage and excision.
These cleaned single strand breaks are then repaired by patch repair, either short or long. Short patch repair replaces the damaged base, whereas long patch repair involves the removal of several bases and then filling in of the gap by DNA polymerase and ligation of the ends.

Nucleotide Excision Repair (NER)

NER is used when a stretch of DNA has been damaged. It is particularly important in the response to ultraviolet radiation, which can cause bulky DNA adducts. The DNA is incised at two points distant from the lesion by 5 - 10 bases, and the entire section of DNA is replaced. The gap in the DNA is then copied from the undamaged side of the DNA strand and ligated onto the free ends.

Mismatch Repair

Mismatch repair is important in carcinogenesis and was described in the DNA Replication topic. Proteins are able to detect abnormal shapes in the DNA due to incorrect pairing of bases. These abnormal bases are excised with a small margin of bases on either side. The gap is then filled by DNA polymerase and the ends ligated.