DNA Repair

Introduction to DNA Repair

  • The most serious outcome of DNA damage is mutation i.e. permanent and heritable change in the genome which may cause cancer, genetic disease.
  • In addition to proof reading activity an elaborate system of DNA repair exists in the body

Types of DNA damage

  • Single base alteration.
    • Depurination
    • Deamination of cytosine to uracil.
    • Deamination of adenine to     hypoxanthine
    • Alkylation of bases (6 methyl guanine)   
    • Base analog incorporation( Bromo uracil)

Types of DNA damage

  • Two base alteration
    • UV light induced lesion(Pyr. Dimer)
  • Chain break.
    • Ionizing radiation ( X-ray)
    • Radioactive disintegration of back bone.
    •   Oxidative free radical formation (oxidation of DNA occurs)

Types of DNA damage

  • Cross linkage
  • Between bases in same or opposite       strand.
  • Between DNA and protein molecules.

Types of DNA repair

1) Mismatch repair.      

2) Base excision repair

3) Nucleotide excision repair.

4) Double strand break repair.

5) Direct repair.

6) Recombination repair.

7)SOS repair

Mismatch repair

  • These are rare mistakes left over even after proof reading, e.g. C could be present opposite A. 
  • The repairing system must distinguish between the template strand and the new strand containing the wrong base.
  • This is accomplished by tagging the template strand with methyl group ( CH3).
  • Three proteins -> Mut S, MutL and Mut H are needed for strand recognition.
  • DAM methylase methylates the template strand. 
  • An endonuclease will cut the strand near the defect.
  • An exonuclease will digest the strand removing the faulty sequence.
  • The gap is filled up by DNAP III, SSB, helicase and ligase.

Base excision repair

  • Spontaneous, chemical, radiation or heat may damage a single base, e.g. 
  • Deamination of adenine to hypoxanthine.
  • Guanine to 6 methyl guanine.
  • Uracil to 5 bromo uracil.
  • Purine to amino purine.
  • There is a class of enzyme called DNA glycosylase that removes the affected base. This creates an apurinic or apyrimidinic site ( AP site ).
  • AP endonuclease cuts the strand containing the defective site.
  • Proper base is replaced by DNA polymerase 1 ( DNAPβ in eukaryotes.)
  • DNA ligase causes final ligation.

Nucleotide excision repair

  • Chemicals, radiation or heat may damage a segment of DNA up to 30 bases. 
  • The enzyme is ABC excinuclease.
  • The enzyme hydrolyzes two phospho diester bonds containing the defect.
  • Synthesis of new strand by DNAP1 ( β in eukaryotes). 
  • Final joining by DNA ligase.

Double strand break repair

  • May occur by ionising radiation, chemo therapeutic agents.
  • Two proteins are involved KU, and DNA PK which bind to the free ends and allow approximation of two ends.
  • Unwinding of the ends by helicase activity of KU. Unwound approximated ends form base pairs, the extra tails are removed by exonuclease.


  • In this process the modified base is reconverted directly to its original form.
  • For example if pyrimidine dimer is formed, the enzyme photolyase (methyl transferase) cleaves the dimer to change it into the original monomeric pyrimidine residues.

Recombination Repair

  • This occurs when DNA undergoes replication before the lesion has been repaired. The replication machinery halts when it encounters a lesion and resumes polymerization beyond the block. 
  • The result of this process is that the daughter strand has large gap opposite the lesion. The gap is repaired by the process of recombination.

Recombination Repair

  • Excision of an undamaged DNA segment from the opposite parental strand.Insertion of excised DNA into the gapped strand.
  • Polymerase 1and Ligase joins this inserted piece to adjacent region.
  • The gap in the parental strand is repaired.
  • The lesion in the original strand is repaired by nucleotide excision repair.


  • This type of repair induces a special set of enzymes at the cost of fidelity of replication , permitting the replication to synthesize DNA opposite the damaged template strand . 
  • The chain synthesis is possible because the editing system is relaxed.
  • The result is often mutation.

DNA repair and Cancer

  • Human cancer develops when certain genes that regulate normal cell division (tumor suppressor gene or proto oncogene) fail or altered.
  • Cells may grow out of control and form a tumor. 
  • Defects in the genes encoding the proteins of different repair systems have been linked to human cancer.

Xeroderma pigmentosum

  • Defective nucleotide excision repair.  
  • UV light -> damaged DNA -> not repaired due to defective NE repair -> replication of damaged DNA -> daughter DNA with mutation -> mutated DNA mediates cancer by activation of protooncogens -> multiple skin cancer.


  • HNPCC -> defective mismatch repair.
  • Cockayne’s syndrome -> defective NE repair.
  • Ataxia telangiectasia -> defect in double strand break repair.
  • Fanconi’s anemia -> lethal aplastic anemia due to defective double strand break repair.

Other Biochemistry Notes

. Biochemistry of Proteins

Carbohydrate Metabolism


Vitamin A

Pyrimidine metabolism

Purine Metabolism

Cardiac Biomarkers


. Blood Metabolism (Heme synthesis and breakdown)

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