As a crucial and early event in the DNA repair process, DNA damage recognition involves complex protein-DNA and protein-protein interactions. Our single-molecule spectroscopy study reveals dynamics of fluctuating molecular non-covalent interactions within single XPA-DNA complexes that are involved in the DNA (NER) damage recognition processes. These results have facilitated a molecule-level understanding of the dynamics and mechanisms of the damage-recognition process in DNA repair. We observed fluorescence-intensity fluctuations in single XPA-DNA complexes at two different time-scales. We concluded that the fast conformational change coordinates are associated with DNA structural fluctuations, but slow conformational coordinates are attributed to interactive motions of the XPA-DNA complex at the binding site, a finding consistent with XPA’s ability to recognize a wide variety of DNA lesions. The required, slow and large-amplitude conformational motions of XPA-DNA complexes have not been reported previously. Approximately 10-fold variation occurs in the rates of the slow interactive conformational motions among the individual complexes. This inhomogeneity is most likely associated with the existence of different subsets of protein conformations seeking an induced-fit to a conformationally fluctuating DNA lesion. Conformational dimensionality reduction, fly-casting driven by induced-fit, water and ion exclusion, DNA and peptide chain diffusive relaxation, protein interior packing relaxation, and hydrogen bond formations are all likely associated with the potential barriers for the trapped interactive states. These trapped and slow-fluctuating interactions could be crucial in XPA-DNA interaction dynamics and intrinsically pertinent to the protein-DNA complexes in other DNA damage recognition processes.
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