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Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair
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DNA lesion alters global conformational dynamics of Y-family DNA polymerase during catalysis

Brian A Maxwell1, Cuiling Xu, Zucai Suo

  • 1Biophysics Program, The Ohio State University, Columbus, Ohio 43210, USA.

The Journal of Biological Chemistry
|February 25, 2012
PubMed

Insights

DNA polymerase IV (Dpo4) efficiently and faithfully bypasses 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), a major DNA lesion. Dpo4 alters its global conformational dynamics to replicate undamaged versus damaged DNA, preventing mutations.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Oxidative damage to DNA produces 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG).
  • Unfaithful bypass of 8-oxoG by DNA polymerases can lead to genomic mutations.
  • Y-family DNA polymerases are involved in DNA repair and translesion synthesis.

Purpose of the Study:

  • To investigate the mechanism by which DNA polymerase IV (Dpo4) bypasses 8-oxoG.
  • To determine if Dpo4 exhibits different conformational dynamics when replicating undamaged versus damaged DNA.
  • To elucidate the role of Dpo4's conformational changes in faithful DNA lesion bypass.

Main Methods:

  • Pre-steady-state kinetic studies.
  • Stopped-flow Förster resonance energy transfer (FRET) studies.
  • Biophysical analysis of DNA polymerase conformational dynamics.

Main Results:

  • DNA polymerase IV (Dpo4) efficiently and faithfully bypasses 8-oxoG.
  • Dpo4 exhibits distinct global conformational dynamics during 8-oxoG bypass and extension compared to undamaged DNA replication.
  • Nucleotide binding-induced translocation of Dpo4 is hindered by 8-oxoG interactions during the extension step.

Conclusions:

  • Y-family DNA polymerases employ altered global conformational dynamics for replicating damaged DNA.
  • Dpo4's adaptive conformational changes are crucial for efficient and faithful 8-oxoG bypass.
  • Understanding these mechanisms is vital for preventing DNA damage-induced mutations.

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