DNA repair - genome stability

Explain in general terms the intrinsic and extrinsic factors that affects genome stability, and the positive and negative consequences of genome stability

Factors decreasing genome stability:

  • Mistakes when copying DNA

  • DNA damage

  • Programmed changes to DNA structure/sequences

Factors maintaining genome stability:

  • High fidelity DNA replication

  • Mismatch repair

  • Homologous recombination

  • Non-homologous end joining

  • Nucleotide excision repair

  • Base excision repair

  • Direct reversal

More genome stability means less likely to develop cancer and less harmful mutations. However genome instability also gives rise to diversity in the immune system (specific antibodies) and positive mutations that can lead to evolution.

Explain the consequences of various types of DNA damage on genome function and understand the difference between DNA damage and mutation

DNA damage is any change to the sequence or structure in DNA. DNA damage may be mutagenic - if not repaired and replicated will lead to a mutation (a permanent change in DNA sequence), or cytotoxic - where the damage means DNA cannot be replicated or transcribed and results in cell death.

Describe a variety of different types of damaged DNA bases

  • Spontaneous hydrolytic damage

    • This occurs when the N-glycosyl bond between a base and deoxyribose breaks leaving an abasic site (AP site). This occurs to G and A (purines) most commonly.

    • Also when cytosine is deaminated (amine group is hydrolysed) forming uracil. Uracil base pairs with A so if left unrepaired, it can introduce a mutation in replication. If the cytosine is methylated, than deamination will produce thymine which is more difficult for the cellulatr machinary to detect and is also mutagenic.

  • Alkylation

    • Alkylating agents are reactive compounds that can transfer methyl or ethyl froups to a DNA base. Methylation of guanine at the O6 position to form O6-methylguanine is an example of DNA damage as it base pairs with thymine. This is therefore mutangenic.

  • Spontaneous oxidative damage

    • Reactive oxygen species are a product of metabolism and can cause DNA lesions, for example, 8-oxo-guanine. 8-oxo-guanine base pairs ambiguously with cytosine or adenine so can be mutagenic.

  • Carcinogens

    • For example, benzopyrene is metabolised and modifies guanine and blocks DNA replication and transcription

  • UV light-induced damage

    • UV light can induce the formation of bonds between pyrimidines stacked on top of each other forming a cyclobutane pyrimidine dimer (CPD). This blocks replication and transcription

  • Chemotherapeutic agent

    • Cisplatin links 2 adjacent guanines in replicating DNA blocking replication and transcription and causing cell death. Used to treat cancer

Explain the mechanism of DNA repair by direct reversal

  • Repair of UV-induced photoproducts

    • DNA photolyases are specific to DNA legions cause by UV light. They use visible light to reverse the damage (photoreactivation). These are not present in humans or other placental mammals.

  • Repair of alkylated bases

    • DNA-alkyltransferases have a catalytic cysteine which they use to remove the methyl group from DNA. This is a suicide reaction as the protein does return to its original form and must be degraded.