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#nucleotide excision repair

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Repair Pathway

Length of DNA removed during prokaryotic NER is approximately

Size of excised patch in nucleotide excision repair defined by positions of UvrC cuts relative to lesion creating specific oligonucleotide length. In Escherichia coli UvrC cuts at 8th phosphodiester bond 5' to lesion and 4th-5th bond 3' to lesion, releasing 12-13 nucleotide fragment bearing bulky adduct, which is removed by UvrD helicase. This short patch is sufficient to eliminate thymine dimers while minimizing resynthesis burden. Eukaryotic NER excises larger 24-32 nucleotide fragment due to larger open complex involving XPB and XPD helicases requiring broader bubble for dual incision by XP

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 5: Length of DNA Excised in Prokaryotic NER

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Repair Pathway

UvrC protein functions as

Prokaryotic NER incision step requires UvrC protein possessing two distinct nuclease domains. N-terminal GIY-YIG domain and C-terminal RNase H-like domain coordinate magnesium ions to cleave phosphodiester bonds at defined distances from lesion. After UvrAB creates open complex around damage verifying lesion, UvrC binds and makes 3' incision 4-5 nucleotides downstream and 5' incision 8 nucleotides upstream generating 12-13 nucleotide oligonucleotide containing damage. It therefore acts as dual endonuclease not helicase, ligase, or polymerase. Helicase activity resides in UvrB and UvrD removing

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 12: UvrC Function as Endonuclease in NER

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Repair Pathway

NER in E. coli recognizes DNA damage by sensing

Nucleotide excision repair deals with bulky lesions causing significant helical distortion such as pyrimidine dimers and benzo[a]pyrene adducts. In E. coli UvrA dimer with ATPase activity scans DNA recognizing distortion rather than specific chemical modification, recruiting UvrB helicase that verifies lesion and forms pre-incision complex. Damage recognition relies on changes in bendability, destabilized duplex, and altered thermodynamics not methylation or replication fork association. Once damage verified, UvrC endonuclease makes dual incisions flanking lesion. This distortion sensing allow

Ref: Watson et al., Molecular Biology of the Gene, 7th ed., Chapter 10: NER Recognition of Helix Distortion by UvrABC

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