Replication Protein A (RPA) is the most abundant single-stranded DNA (ssDNA) binding protein in eukaryotes. RPA is involved in key DNA metabolic processes, including replication and repair, which makes understanding its binding kinetics essential. RPA has six DNA binding domains, each with different affinities for binding to ssDNA. Individual binding domains may disassociate while others are bound, creating a dynamic binding process. Using a single-molecule fluorescence-based assay, we observed a systematic shift in the binding conformation of RPA as a function of salt concentration. The distributions of conformations at all salt concentrations were heterogeneous but were dominated by two states. This suggests certain binding domains dissociate from DNA earlier than others as the salt concentration is increased, highlighting the complicated nature of the RPA-ssDNA interactions.
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