Deciphering the mechanism of processive ssDNA digestion by the Dna2-RPA ensemble

Jiawei Ding#, Xiangting Li#, Jiangchuan Shen#, Yiling Zhao, Hengyao Niu*, and Zhi Qi* (#Equal contribution, *Corresponding authors)

Nature Communications volume 14, Article number: 3864 (2023)
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The eukaryotic single-stranded DNA (ssDNA)-binding protein Replication Protein A (RPA) plays a crucial role in various DNA metabolic pathways, including DNA replication and repair, by dynamically associating with ssDNA. While the binding of a single RPA molecule to ssDNA has been thoroughly studied, the accessibility of ssDNA is largely governed by the bimolecular behavior of RPA, the biophysical nature of which remains unclear. In this study, we develop a three-step low-complexity ssDNA Curtains method, which, when combined with biochemical assays and a Markov chain model in non-equilibrium physics, allow us to decipher the dynamics of multiple RPA binding to long ssDNA. Interestingly, our results suggest that Rad52, the mediator protein, can modulate the ssDNA accessibility of Rad51, which is nucleated on RPA coated ssDNA through dynamic ssDNA exposure between neighboring RPA molecules. We find that this process is controlled by the shifting between the protection mode and action mode of RPA ssDNA binding, where tighter RPA spacing and lower ssDNA accessibility are favored under RPA protection mode, which can be facilitated by the Rfa2 WH domain and inhibited by Rad52 RPA interaction.



Ding, J., Li, X., Shen, J. et al. ssDNA accessibility of Rad51 is regulated by orchestrating multiple RPA dynamics. Nat Commun 14, 3864 (2023).