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:

1. 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.

2. 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.

3. 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.

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.

• Base Excision Repair (BER) - A cellular process that repairs damaged DNA.
• Long Patch BER - A BER variant that repairs multiple bases at the damaged site.
• Short Patch BER - A BER variant that repairs a single base at the damaged site.
• Photoreactivation Repair - Recovery of cellular DNA damaged by sunlight.
• Endonuclease - An enzyme that cuts DNA strands internally at the site of damage.

• Define Base Excision Repair (BER) – Explain what it is (e.g., BER).
• Contrast Long Patch vs Short Patch – Explain key differences (e.g., the length of repair).
• Explore Photoreactivation Repair – Describe scenario (e.g., when light-damaged DNA is repaired).
• Explain Endonuclease Process – A detailed description of how endonuclease cuts DNA strands.
• Apply in Context – The relevance of DNA repair in cellular health and disease.

• [Question 1] What is Base Excision Repair and how does it happen?
• [Question 2] How does Long Patch differ from Short Patch?
• [Question 3] What is Endonuclease and its role in DNA repair?

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• Educators – Provides a comprehensive and detailed content ideal for teaching molecular biology.
• Researchers – Deeply relevant to studies of DNA repair, genetics, and related fields.
• Science Enthusiasts – Offers valuable insight into the intricate workings of cellular DNA repair.