Nucleosome unwrapping and PARP1 allostery drive affinities for chromatin and DNA breaks

Schaich, M. A.; Weaver, T. M.; Rakowski, J. A.; Roginskaya, V.; Leary, L. P.; van den Berg, A. A.; Iwasa, J. H.; Freudenthal, B. D.; Van Houten, B.

doi:10.1101/2025.08.29.673134

bioRxiv · 10.1101/2025.08.29.673134

Nucleosome unwrapping and PARP1 allostery drive affinities for chromatin and DNA breaks

Schaich, M. A.·Weaver, T. M.·Rakowski, J. A.·Roginskaya, V.·Leary, L. P.·van den Berg, A. A.·Iwasa, J. H.·Freudenthal, B. D.·Van Houten, B.

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Abstract

Poly[ADP-ribose] polymerase 1 (PARP1) detects DNA strand breaks that occur in duplex DNA and chromatin. We employed correlative optical tweezers and fluorescence microscopy to quantify how single molecules of PARP1 identify single-strand breaks (i.e., nicks), undamaged nucleosome core particles (NCP) and NCPs containing DNA nicks. Fluorescently-tagged PARP1 or PARP2 from nuclear extracts bound nicks with nanomolar affinity but did not engage undamaged dsDNA regions. In contrast, PARP1 avidly bound undamaged NCPs, and partial NCP unwrapping induced by DNA tension significantly increased the on rate and affinity. Catalytically dead PARP1 or EB-47 inhibition greatly increased PARP1 affinity to DNA nicks and undamaged NCP, implicating a mechanism where PARP1 reverse allostery regulates PARP1 retention to undamaged chromatin. We also monitored ADP-ribosylation in real time upon PARP1 binding undamaged or nicked NCPs. These results provide key mechanistic insights into domain allostery and how pharmacological intervention alters PARP1 binding dynamics for therapeutic impacts.

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Schaich, M. A., Weaver, T. M., Rakowski, J. A., Roginskaya, V., Leary, L. P., van den Berg, A. A., Iwasa, J. H., Freudenthal, B. D., Van Houten, B.. 2025-08-31. Nucleosome unwrapping and PARP1 allostery drive affinities for chromatin and DNA breaks. https://doi.org/10.1101/2025.08.29.673134

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