Slide 2:

• Nucleotide Excision Repair (NER)

• Definition and purpose

• Steps involved in NER

  1. Recognition of DNA damage

  2. Excision and removal of damaged DNA strand

  3. Repair synthesis and ligation

• Example of a disorder related to NER: Xeroderma pigmentosum

Slide 3:

• Base Excision Repair (BER)

• Definition and purpose

• Steps involved in BER

  1. DNA glycosylase recognition and base removal

  2. AP endonuclease and DNA polymerase activity

• Example involving BER: Repair of oxidative DNA damage

Slide 4:

• Mismatch Repair (MMR)
• Definition and purpose
• Importance of MMR in maintaining genomic integrity
• Steps involved in MMR

  1. Mismatch recognition

  2. Strand discrimination and excision

  3. Resynthesis and ligation

Slide 5:

• Photoreactivation Repair (PRE)
• Definition and purpose
• Role of photolyase enzyme in PRE
• Light-dependent repair mechanism
• Example of a organism capable of PRE: E. coli

Slide 6:

• Homologous Recombination (HR)

• Definition and purpose

• Key steps involved in HR

  1. DNA double-strand break formation

  2. Strand invasion and pairing

  3. Holliday junction formation and resolution

• Example involving HR: Repair of DNA breaks during meiosis

Slide 7:

• Non-Homologous End Joining (NHEJ)

• Definition and purpose

• Steps involved in NHEJ

  1. DNA double-strand break recognition

  2. End processing and ligation

• Example of a disorder related to NHEJ: Severe combined immunodeficiency (SCID)

Slide 8:

• Direct Repair Mechanisms
• O6-Methylguanine methyltransferase (MGMT) repair mechanism
• Alkyltransferases and their role in direct repair
• Example involving direct repair: Removal of methyl or ethyl groups from DNA bases

Slide 9:

• Translesion Synthesis (TLS)
• Definition and purpose
• How TLS bypasses DNA lesions
• Error-prone nature of TLS and its significance
• Example involving TLS: UV-induced DNA damage repair

Slide 10:

• Summary of DNA Repair Mechanisms
• Importance of DNA repair in maintaining genomic stability
• Key mechanisms discussed: NER, BER, MMR, PRE, HR, NHEJ, Direct Repair, TLS
• Role of each repair mechanism in different types of DNA damage
• Application of DNA repair mechanisms in various fields, such as medicine and biotechnology

11. DNA Damage and Repair

• DNA damage can be caused by various factors such as radiation, chemicals, and errors during DNA replication.
• The human body has evolved several mechanisms to repair DNA damage and maintain genomic integrity.
• DNA repair mechanisms are crucial for preventing mutations and maintaining normal cellular functions.
• Failure in DNA repair mechanisms can lead to genetic disorders and increased risk of cancer.
• The excision repair system is one of the major DNA repair mechanisms.

12. Nucleotide Excision Repair (NER)

• NER is a DNA repair mechanism that deals with bulky lesions, including UV-induced pyrimidine dimers.
• This repair mechanism involves several proteins, including endonucleases, helicases, and DNA polymerases.
• The NER process can be divided into two sub-pathways: transcription-coupled repair (TC-NER) and global genome repair (GG-NER).
• TC-NER primarily focuses on repairing DNA lesions in active genes, while GG-NER repairs lesions throughout the genome.
• Xeroderma pigmentosum is a genetic disorder caused by defects in NER genes.

13. Base Excision Repair (BER)

• BER is a DNA repair mechanism that deals with minor base damage, such as alkylation and oxidation.
• The BER pathway involves recognition and removal of damaged bases by DNA glycosylases.
• After base removal, AP endonucleases and DNA polymerases come into play to replace the damaged base with the correct one.
• BER is essential for maintaining genomic stability and preventing mutagenesis.
• Oxidative DNA damage, caused by reactive oxygen species, is repaired through BER.

14. Mismatch Repair (MMR)

• MMR is a DNA repair mechanism that corrects errors that occur during DNA replication.
• MMR is responsible for recognizing and removing mispaired bases and small insertions or deletions (indels).
• Defects in MMR genes can lead to a condition called Lynch syndrome, which predisposes individuals to various types of cancer.
• MMR is crucial for maintaining the fidelity of DNA replication and preventing the accumulation of mutations.
• MMR also plays a role in repairing DNA damage caused by certain chemicals and drugs.

15. Photoreactivation Repair (PRE)

• PRE is a DNA repair mechanism found in some organisms, including bacteria and plants.
• PRE utilizes the enzyme photolyase, which uses light energy to repair UV-induced DNA damage, such as pyrimidine dimers.
• Photolyase breaks the covalent bond between the damaged bases, restoring the DNA strand to its original state.
• PRE is a direct repair mechanism that does not involve the removal or synthesis of nucleotides.
• E. coli is a well-known example of an organism capable of PRE.

16. Homologous Recombination (HR)

• HR is a DNA repair mechanism that repairs DNA double-strand breaks (DSBs) and ensures the correct alignment of homologous DNA sequences.
• HR involves the exchange of DNA strands between homologous chromosomes or sister chromatids.
• The RAD51 protein plays a key role in HR by facilitating strand invasion and the formation of Holliday junctions.
• HR is crucial for repairing DSBs during meiosis, as it allows for genetic recombination and the generation of genetic diversity.
• HR also plays a role in repairing DSBs induced by ionizing radiation.

17. Non-Homologous End Joining (NHEJ)

• NHEJ is another DNA repair mechanism for repairing DNA double-strand breaks.
• NHEJ is an error-prone repair process that directly joins the broken ends of the DNA without requiring a homologous template.
• The Ku protein complex is essential for the initial recognition and binding of DNA ends in NHEJ.
• NHEJ can introduce small indels or deletions at the repair site, leading to potential mutations.
• Mutations in NHEJ genes can result in severe combined immunodeficiency (SCID).

18. Direct Repair Mechanisms

• Direct repair mechanisms involve the removal of specific DNA lesions without the need for excision or synthesis steps.
• One example of direct repair mechanism is the O6-Methylguanine methyltransferase (MGMT) repair system.
• MGMT removes and repairs alkyl groups, such as methyl or ethyl groups, from specific DNA bases.
• Direct repair mechanisms are fast and efficient, allowing for the direct reversal of specific DNA lesions.
• Direct repair mechanisms are important for preventing mutations and maintaining genomic stability.

19. Translesion Synthesis (TLS)

• TLS is a DNA repair mechanism that bypasses DNA lesions, such as bulky adducts or crosslinks.
• TLS involves specialized DNA polymerases that can replicate across damaged DNA templates.
• TLS is an error-prone repair pathway, as the specialized polymerases have relaxed fidelity and can introduce mutations.
• Despite being error-prone, TLS is crucial for ensuring DNA replication can continue in the presence of DNA lesions.
• UV-induced DNA damage is repaired through TLS in order to prevent DNA replication arrest.

20. Summary and Applications

• DNA repair mechanisms play a vital role in maintaining genomic stability and preventing the accumulation of mutations.
• The excision repair system, including NER, BER, MMR, PRE, HR, NHEJ, direct repair, and TLS, ensures the integrity of the genetic material.
• Genetic disorders, such as xeroderma pigmentosum and Lynch syndrome, can result from defects in DNA repair mechanisms.
• Understanding DNA repair mechanisms has important implications in various fields, including medicine, genetics, and biotechnology.
• Further research in DNA repair mechanisms may lead to the development of novel therapies and interventions for diseases related to DNA damage.

21. Importance of DNA Repair Mechanisms

• DNA repair mechanisms are crucial for maintaining genomic integrity and preventing the accumulation of mutations.
• Mutations in DNA can lead to various genetic disorders and an increased risk of cancer.
• Without efficient DNA repair mechanisms, genetic information could be lost or distorted during DNA replication or as a result of DNA damage.
• DNA repair systems help in preserving the genetic code and ensuring its accurate transmission to future generations.
• Understanding DNA repair mechanisms is essential for studying diseases related to DNA damage and developing strategies for their prevention and treatment.

22. Types of DNA Damage

• DNA damage can occur due to various factors, including environmental agents, chemicals, radiation, and errors during DNA replication.
• Types of DNA damage include:
  1. Base damage: Modifications or loss of DNA bases, such as alkylation, oxidation, deamination, or depurination.
  2. DNA strand breaks: Single-strand breaks (SSBs) and double-strand breaks (DSBs) can occur due to various causes.
  3. Crosslinking: Covalent linkages between DNA strands can prevent proper DNA replication and transcription.
  4. Bulky adducts: Large chemical modifications or lesions that distort the DNA helix, such as pyrimidine dimers induced by UV radiation.
  5. Misincorporation errors: Incorrect pairing of nucleotides during DNA replication, leading to DNA mismatches.

23. Overview of the Excision Repair System

• The excision repair system comprises several repair pathways that remove and replace damaged DNA bases or fragments.
• Key repair pathways include nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), and direct repair.
• Each pathway has specific enzymes and proteins involved in recognizing, removing, and replacing damaged DNA.
• The excision repair system operates on a wide range of DNA lesions and ensures the faithful repair of DNA damage.
• Defects in any of these repair pathways can have serious consequences, including genetic diseases and cancer susceptibility.

24. Nucleotide Excision Repair (NER)

• NER is a versatile DNA repair mechanism that removes bulky DNA lesions, such as pyrimidine dimers induced by UV radiation.
• The process involves several steps:
  1. Recognition of DNA damage: Damage recognition proteins detect and bind to the damaged DNA region.
  2. Excision and removal of damaged DNA strand: Endonucleases make incisions on both sides of the damaged region, removing a small fragment.
  3. Repair synthesis and ligation: DNA polymerase synthesizes a new DNA strand using the undamaged strand as a template, followed by ligation.
• NER operates in two sub-pathways: transcription-coupled repair (TC-NER) and global genome repair (GG-NER).

25. Example of a Disorder related to NER: Xeroderma Pigmentosum

• Xeroderma pigmentosum (XP) is a genetic disorder characterized by extreme sensitivity to UV radiation.
• Individuals with XP have defects in NER genes, leading to an impaired ability to repair UV-induced DNA damage.
• Lack of functional NER results in a high risk of developing skin cancers and other UV-related complications.
• XP demonstrates the critical role of NER in protecting against DNA damage caused by environmental factors.
• Early diagnosis and protection from UV radiation are essential for individuals with XP to prevent disease progression.

26. Base Excision Repair (BER)

• BER is a DNA repair mechanism that primarily deals with small base lesions, such as alkylation or oxidative damage.
• The process involves several steps:
  1. DNA glycosylase recognition and base removal: Glycosylase enzymes detect and remove the damaged base, cleaving the glycosylic bond.
  2. AP endonuclease and DNA polymerase activity: AP endonuclease makes an incision in the DNA backbone, followed by DNA polymerase filling the gap.
• BER is critical for maintaining genomic stability by repairing damaged bases before errors occur during DNA replication.

27. Example Involving BER: Repair of Oxidative DNA Damage

• Oxidative stress can cause DNA damage through the generation of reactive oxygen species (ROS).
• Oxidative DNA damage includes the oxidation of guanine bases, leading to the formation of 8-oxoguanine lesions.
• BER plays a crucial role in repairing such oxidative DNA damage by removing the damaged base and replacing it with the correct base.
• Failure to repair oxidative DNA damage can lead to mutations, genomic instability, and increased risk of diseases, including cancer and neurodegenerative disorders.
• BER ensures the faithful restoration of DNA integrity and the prevention of mutagenesis caused by oxidative stress.

28. Mismatch Repair (MMR)

• MMR is a DNA repair mechanism that corrects errors that occur during DNA replication, ensuring the accuracy of DNA synthesis.
• The process involves several steps:
  1. Mismatch recognition: Mismatch repair proteins identify and bind to mismatches or small indels.
  2. Strand discrimination and excision: The strand carrying the error is preferentially targeted for excision.
  3. Resynthesis and ligation: DNA polymerase fills the gap with the correct bases, followed by ligation.
• MMR is crucial for preventing the accumulation of mutations and maintaining the fidelity of DNA replication.

29. Example involving MMR: Repair of DNA Mismatches

• DNA mismatches can occur due to errors during DNA replication or recombination.
• MMR plays a key role in correcting DNA mismatches and preventing the persistence of errors in the genome.
• MMR defects can result in a condition called Lynch syndrome, characterized by an increased risk of colorectal and other cancers.
• The loss of MMR function leads to microsatellite instability, a hallmark of Lynch syndrome and some sporadic cancers.
• Understanding MMR mechanisms provides insights into genetic instability and the development of targeted therapies for MMR-related cancers.

30. Summary

• The excision repair system is a complex network of DNA repair mechanisms that ensure the faithful restoration of DNA integrity.
• NER repairs bulky DNA lesions, such as UV-induced pyrimidine dimers, through a multistep process.
• BER deals with small base damage, such as alkylation or oxidative damage, by removing and replacing damaged bases.
• MMR corrects DNA mismatches that occur during DNA replication, maintaining the fidelity of the genetic code.
• Defects in any of these repair mechanisms can have severe consequences, leading to genetic disorders and an increased risk of cancer.
• Understanding DNA repair mechanisms is vital for studying diseases related to DNA damage and developing therapeutic interventions.