DNA Damage and Repair Mechanisms

Study Notes

Endogenous DNA damage arises from internal chemical reactions within cells.
Replication errors are a source of endogenous damage occurring during replication. Incorrect nucleotides are incorporated opposite template bases. Some DNA polymerases, with lower fidelity, may be involved, leading to errors.
Topoisomerases are another source of endogenous DNA damage. They remove DNA supercoiling during replication and transcription. Misalignment of DNA ends can stabilize topoisomerase-DNA cleavage complexes, creating DNA lesions.
Reactive oxygen species (ROS) are produced during cellular processes. ROS can cause oxidative DNA damage. While ROS plays a role in normal cellular function, excessive levels result in DNA lesions and modifications. Excessive ROS is linked to diseases like cancer, Alzheimer's, and diabetes.

Direct reversal repair is a DNA repair mechanism that directly fixes specific types of damage. It does not require excision or replacement.
UV-induced lesions (thymine dimers) caused by UV light can be reversed via photoreactivation. This process uses visible light energy to break the damaged DNA structure and restore the original pyrimidine bases. DNA photolyases mediate this reaction using energy from absorbed light.
Pyrimidine dimers result from UV-induced reactions. Photolyases use energy from absorbed light to reverse these damage types.

BER is a DNA repair pathway, exemplified by repairing uracil-containing DNA.
DNA glycosylase recognizes and removes the uracil base.
This creates an AP site (apurinic/apyrimidinic site), a gap in the DNA strand.
AP endonuclease cleaves the gap. The remaining sugar is removed.
The gap is filled in by DNA polymerase.
The nick is sealed via DNA ligase.
BER involves steps such as recognition of damaged base, removal of base, cleavage of AP site, removal of sugar, gap filling using polymerase, and sealing with ligase.

MMR involves protein complexes, like MSH2-MSH6 ( MutS). MMR proteins locate mismatch errors to facilitate further repair.
MutS and MutL are important proteins in eukaryotes. In prokaryotes (E. coli), MutH also plays a role.
Exonuclease 1 (Exo1) degrades the error-containing strand during replication. Replication protein A (RPA) protects from further DNA degradation by binding to exposed DNA.
DNA polymerase makes the correct sequence. DNA ligase seals any remaining nicks in the repaired DNA.
Mutations in MMR genes can cause Lynch syndrome, a hereditary condition associated with increased risk of colon, ovarian, and other cancers.