A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA

Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5752-7. doi: 10.1073/pnas.0509723103. Epub 2006 Apr 3.

Abstract

A central mystery in the function of site-specific DNA-binding proteins is the detailed mechanism for rapid location and binding of target sites in DNA. Human oxoguanine DNA glycosylase 1 (hOgg1), for example, must search out rare 8-oxoguanine lesions to prevent transversion mutations arising from oxidative stress. Here we report high-speed imaging of single hOgg1 enzyme molecules diffusing along DNA stretched by shear flow. Salt-concentration-dependent measurements reveal that such diffusion occurs as hOgg1 slides in persistent contact with DNA. At near-physiologic pH and salt concentration, hOgg1 has a subsecond DNA-binding time and slides with a diffusion constant as high as 5 x 10(6) bp(2)/s. Such a value approaches the theoretical upper limit for one-dimensional diffusion and indicates an activation barrier for sliding of only 0.5 kcal/mol (1 kcal = 4.2 kJ). This nearly barrierless Brownian sliding indicates that DNA glycosylases locate lesion bases by a massively redundant search in which the enzyme selectively binds 8-oxoguanine under kinetic control.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Substitution
  • Bacteriophage lambda / genetics
  • Binding Sites
  • DNA Damage
  • DNA Glycosylases / chemistry*
  • DNA Glycosylases / metabolism*
  • DNA Repair*
  • DNA, Viral / chemistry
  • DNA, Viral / genetics*
  • Guanine / analogs & derivatives
  • Guanine / metabolism
  • Humans
  • Kinetics
  • Microscopy, Fluorescence
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Nucleic Acid Conformation
  • Protein Conformation
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Substrate Specificity

Substances

  • DNA, Viral
  • Recombinant Proteins
  • 8-hydroxyguanine
  • Guanine
  • DNA Glycosylases
  • oxoguanine glycosylase 1, human