Single molecule analysis reveals monomeric XPA bends DNA and undergoes episodic linear diffusion during damage search

Nat Commun. 2020 Mar 13;11(1):1356. doi: 10.1038/s41467-020-15168-1.

Abstract

Nucleotide excision repair (NER) removes a wide range of DNA lesions, including UV-induced photoproducts and bulky base adducts. XPA is an essential protein in eukaryotic NER, although reports about its stoichiometry and role in damage recognition are controversial. Here, by PeakForce Tapping atomic force microscopy, we show that human XPA binds and bends DNA by ∼60° as a monomer. Furthermore, we observe XPA specificity for the helix-distorting base adduct N-(2'-deoxyguanosin-8-yl)-2-acetylaminofluorene over non-damaged dsDNA. Moreover, single molecule fluorescence microscopy reveals that DNA-bound XPA exhibits multiple modes of linear diffusion between paused phases. The presence of DNA damage increases the frequency of pausing. Truncated XPA, lacking the intrinsically disordered N- and C-termini, loses specificity for DNA lesions and shows less pausing on damaged DNA. Our data are consistent with a working model in which monomeric XPA bends DNA, displays episodic phases of linear diffusion along DNA, and pauses in response to DNA damage.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biophysics / methods
  • DNA / chemistry*
  • DNA / metabolism*
  • DNA Adducts / chemistry
  • DNA Adducts / metabolism
  • DNA Damage / physiology
  • DNA Repair / physiology
  • DNA-Binding Proteins / metabolism
  • Humans
  • Microscopy, Atomic Force
  • Protein Binding
  • Single Molecule Imaging / methods*
  • Ultraviolet Rays
  • Xeroderma Pigmentosum Group A Protein / chemistry*
  • Xeroderma Pigmentosum Group A Protein / metabolism*

Substances

  • DNA Adducts
  • DNA-Binding Proteins
  • XPA protein, human
  • Xeroderma Pigmentosum Group A Protein
  • DNA