Single Molecule Studies of DNA Damage Recognition by XPA

Nucleotide excision repair (NER) is responsible for the repair of a wide range of DNA lesions, including UV-induced photoproducts and bulky base adducts. XPA is an essential protein in eukaryotic NER, although questions about its stoichiometry and mechanism of damage recognition have been heretofore unresolved. Regions of intrinsic disorder within the N- and C-termini of XPA have made structural work on the full-length protein challenging and compel an alternative approach. We have used PeakForce Tapping® atomic force microscopy to show that human XPA binds to DNA as a monomer and bends it ~60°. Furthermore, XPA demonstrated specificity for the helix-distorting base adduct, N-(2’-deoxyguanosin-8-yl)-2-acetylaminofluorene. Single molecule fluorescence microscopy revealed that DNA-bound XPA exhibits multiple modes of linear diffusion between paused phases. These included long distance motion with rapid diffusion (D ≈ 0.04 μm2/s) consistent with hopping and short distance motion (D ≈ 0.0003 μm2/s) consistent with sliding along the DNA contour. The presence of DNA damage increases pausing by proteins undergoing one-dimensional target search. A truncated mutant, lacking most of the intrinsically disordered regions and made up of just residues 98-239 of the DNA binding domain, exhibits less pausing on UV-damaged DNA compared to the full length protein. In summary, our data are consistent with a model in which the conformational state of XPA is dependent upon the presence of DNA damage and bending