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

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.