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Beckwitt, Emily C.; Jang, Sunbok; Detweiler, Isadora Carnaval; Kuper, Jochen; Sauer, Florian; Simon, Nina; Bretzler, Johanna; Watkins, Simon C.; Carell, Thomas; Kisker, Caroline and Houten, Bennett van (2020): Single molecule analysis reveals monomeric XPA bends DNA and undergoes episodic linear diffusion during damage search. In: Nature Communications, Vol. 11, No. 1, 1356 [PDF, 3MB]


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 similar to 60 degrees 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. It is not fully understood how XPA interacts with a DNA lesion during nucleotide excision repair. Here, the authors use single molecule analysis to study XPA-DNA interactions, including the DNA bend angle, protein stoichiometry, and diffusive properties during damage search.

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