DNA Damage Repair Mechanisms PDF

Dr/ Amany Hamed 1. Endogenous DNA Damage ❑ Endogenous DNA damage originates from internal reactions involving chemically active DNA within cells. ✓ Replication errors are one source of endogenous DNA damage that occurs during DNA replication when incorrect nucleoti...

Dr/ Amany Hamed 1. Endogenous DNA Damage ❑ Endogenous DNA damage originates from internal reactions involving chemically active DNA within cells. ✓ Replication errors are one source of endogenous DNA damage that occurs during DNA replication when incorrect nucleotides are inserted opposite the template bases. During replication, some DNA polymerases with lower fidelity can be involved, leading to potential errors. Dr/ Amany Hamed 1. Endogenous DNA Damage ✓ Topoisomerase enzymes are another source of endogenous DNA damage. Topoisomerases remove the supercoiling of DNA during replication and transcription. However, misalignment of the DNA ends can stabilize the topoisomerase-DNA cleavage complex and result in the formation of DNA lesions. Dr/ Amany Hamed 1. Endogenous DNA Damage ✓ Reactive oxygen species (ROS) are produced during cellular processes and can cause oxidative damage to DNA. While ROS plays an important role in normal cellular functions, excessive levels can lead to various DNA lesions and modifications. Excessive ROS has been associated with the development of several human diseases like cancer, Alzheimer’s disease, and diabetes. Dr/ Amany Hamed 1. Direct reversal repair ❑ Direct reversal repair is a DNA repair mechanism that directly fixes specific types of DNA damage without the need for excision or replacement. ❑ Two examples of DNA damage that can be reversed are UV-induced lesions and alkylated bases. Dr/ Amany Hamed 1. Direct reversal repair ❑ UV-induced lesions (Thymine dimer), caused by UV light, can be reversed through a process called photoreactivation, which uses visible light energy to break the damaged DNA structure, restoring the original pyrimidine bases. ❑ Reaction promoted by DNA photolyases. ❑ Pyrimidine dimers result from a UV-induced reaction, and photolyases use energy from absorbed light to reverse the damage.  Dr/ Amany Hamed 1. Direct reversal repair Figure: Direct repair of UV-induced thymine dimer Dr/ Amany Hamed Base excision repair One example of BER is the repair of uracil- containing DNA. In this process, a DNA glycosylase recognizes and removes the uracil base, creating a gap in the DNA called the AP site. The gap is then cleaved by an enzyme called AP endonuclease. After that, the remaining sugar is removed, and the gap is filled using DNA polymerase and sealed with ligase. Dr/ Amany Hamed Base excision repair 1. A DNA glycosylase recognizes a damaged base and cleaves between the base and deoxyribose in the backbone. 2. An AP endonuclease cleaves the phosphodiester backbone near the AP site. 3. DNA polymerase I initiate repair synthesis from the free 3’ hydroxyl at the nick, removing (with its 5’- 3’ exonuclease activity) and replacing a portion of the damaged strand. 4. The nick remaining after DNA polymerase I has dissociated is sealed by DNA ligase. Dr/ Amany Hamed Base excision repair Dr/ Amany Hamed Nucleotide excision repair The general pathway of nucleotide-excision repair is similar in all organisms. 1. An exonuclease binds to DNA at the site of a bulky lesion and cleaves the damaged DNA strand on either side of the lesion. 2. The DNA segment of 13 nucleotides or 29 nucleotides is removed with the aid of a helicase. 3. The gap is filled in by DNA polymerase, 4. The remaining nick is sealed with DNA ligase. Dr/ Amany Hamed 3. Nucleotide excision repair Dr/ Amany Hamed 3. Mismatch repair ✓ First, protein complexes such as MSH2-MSH6 in the MutS protein locate the mismatch errors which helps in further repair. MutS and MutL are important protein complexes in eukaryotes. In E. coli, another protein MutH also has an important role in mismatch repair. ✓ Next, exonuclease 1 (Exo1) degrades the error-containing strand while replication protein A (RPA) prevents further DNA degradation by binding to the exposed DNA. ✓ Then, DNA polymerase synthesizes the correct sequence. ✓Finally, DNA ligase then seals any remaining nicks in the repaired Dr/ Amany Hamed 3. Mismatch repair ✓Mutations in MMR genes can lead to Lynch syndrome, a hereditary condition associated with an increased risk of colon, ovarian, and other cancers. Dr/ Amany Hamed 3. Mismatch repair