7.3:
Long-patch Base Excision Repair
In mammals, a second type of BER is observed, which is often used preferentially during ATP shortage – long patch BER. Instead of just removing the single damaged base, long-patch BER repairs a patch several nucleotides long.
To achieve this, a different DNA polymerase, δ/ɛ adds several nucleotides that displace the original nucleotides. This results in an overhang of oligonucleotides called a flap, which contains the damaged base.
In the presence of a replication factor called proliferating cell nuclear antigen or PCNA, a special endonuclease called Flap Endonuclease (FEN) removes this flap before a DNA ligase seals the nick.
The mechanism of long patch BER is particularly useful to repair damages resulting from ionizing radiation.
7.3:
Long-patch Base Excision Repair
Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
- Lesion type: Depending on the type of base damage, a specific DNA glycosylase – mono or bifunctional, is recruited to the damaged site. While the sequential action of a monofunctional glycosylase favors long patch repair events, the bifunctional glycosylase drives short-patch BER.
- State of the cell cycle: The major protein participants that distinguish the long-patch BER from the alternative pathway of short-patch BER are proliferating cell nuclear antigen (PCNA), protein replication factor C (RF-C), and the flap structure-specific endonuclease 1 (FEN1). PCNA is particularly recognized as the lynchpin of this pathway. It acts both as the scaffold to anchor the polymerase at the damaged site and binds to FEN-1 to facilitate its nuclease activity. Furthermore, RF-C is required to load the PCNA onto the DNA. All of these proteins are also required during DNA replication, suggesting that long-patch BER mends damages to replicating DNA while short-patch is used for repairing resting DNA.
- ATP shortage: It has also been observed that while single nucleotide or short patch BER predominates under normal physiological conditions, under conditions of ATP shortage, the preference is shifted towards long-patch BER. This is because poly(ADP-ribose) can serve as a unique source of ATP during the ligation step in BER.
Suggested Reading
- Fortini, Paola, and Eugenia Dogliotti. "Base damage and single-strand break repair: mechanisms and functional significance of short-and long-patch repair subpathways." DNA repair 6, no. 4 (2007): 398-409.
- Petermann, Eva, Mathias Ziegler, and Shiao Li Oei. "ATP-dependent selection between single nucleotide and long patch base excision repair." DNA repair 2, no. 10 (2003): 1101-1114.