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Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level

Citation

Michaelis, Jens et al. (2022), Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level, Dryad, Dataset, https://doi.org/10.5061/dryad.66t1g1k3v

Abstract

Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1’s multi-domain organization. Here, we directly probe this fundamental yet poorly understood process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1’s N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state. 

Funding

Medical Research Council, Award: U105178934

Carl-Zeiss-Stiftung