dna repair part 1

• Frequent damage of DNA requires efficient repair

  • Naturally occurring oxidative DNA damages arise at least 10,000 times per cell per day in humans
  • 2,000 to 10,000 depurinations per cell per day, and 55,200 single-strand breaks per cell per day
  • DNA repair is essential
• Sources of mutations:

  • DNA replication errors
  • Chemical damage
• Types of DNA Damage:

  • Deamination of adenine produces hypoxanthine
  • Deamination of guanine produces xanthine
  • Deamination of cytosine produces uracil
  • Depurination by hydrolysis of the N-glycosidic linkage
  • Deamination of methylated cytosine produces thymine
• UV light creates thymine dimers

  • Bases absorb light in the UV range (260 nm), leading to photochemical fusion of two adjacent pyrimidines
  • Pyrimidine dimers block replication
• Main players in mismatch repair:

  • Recognition: MutS (MutH determines the strand)
  • Excision: MutH (activated by MutL) and exonuclease
  • DNA synthesis: DNA Pol III
  • Ligation: DNA ligase
• Mismatch repair in eukaryotes:

  • MSH proteins (MSH2:MSH6 complex) bind the mismatch and identify the newly synthesized strand
  • MLH1 endonuclease and other factors bind, recruiting a helicase + exonuclease to remove several nucleotides including the lesion
  • The gap is filled by Pol δ (lagging strand DNA polymerase) and sealed by DNA ligase
• types of point mutations:

  • transitions: purine:purine or pyrimidine:pyrimidine
  • transversion: purine:pyrimidine or pyrmidine:purine
  • synonymous: point mutation in the third nucleotide where the aminoacid remains the same
  • nonsynonymous: point mutation resulting a different amino acid
  • nonsense: point mutation resulting coding codon turns into a stop codon
  • readthrough: point mutation resulting stop codon turns into a coding codon
• indels:

  mutations that result in a change in the nucleotide sequence of a gene, like insertion or deletion of bases
• microsatellites

  a tract of repetitive DNA in which certain DNA motifs (1-6 base pairs) are repeated 5-50 times. occurs at thousand of locations within an organisms genoms. they hade a higher mutation rate than other areas of DNA leading to high genetic diveristy
• types of DNA damage:

  • deamination of cytosine: produces uracil which is unnatural in DNA, is the most frequent
  • depurination by hyrodlysis of N-glycosidic linkage
  • deamination of methylated cytosine: produces thymine which is natural in DNA
• DNA damage and repair of deamination:

  • deamination of cytosine produces uracil and is repaired be replacing uracil by cytosine by the base excision repair mechanism
  • deamination of methylated cytosine results a thymine and is repaird by resolving G:T mismatched bases to A:T
• pyrimidine dimer

  lesion formed by two pyrmidiner (cytosine or thymine)
• replication error

  • due to tautomeric shifts: spontaneous rearrangment within a molecule, forming an isomer
  • replication can change a misincorporated base into a permanent mutation
  • repair: mismatch repair system
• mismatch repair system in E. coli (summary):

  1. recognition: MutS detects mismatch, MutH determines the strand
  2. excision: MutH and exonuclease
  3. DNA synthesis:DNA pol III
  4. ligation: DNA ligase
• Dam methylation determines what strand to repair

  • Old parental strand is marked with methylation of GATC
  • MutH binds to hemi-methylated sites
  • MutH is activated by MutS+MutL
  • the unmethylated strand is the strand to repair