RPA facilitates rejoining of DNA double-strand breaks in an in vitro assay utilizing genomic DNA as substrate

Abstract

Purpose : Replication protein-A (RPA) is a heterotrimeric single-stranded DNA-binding protein playing essential roles in many aspects of nucleic acid metabolism, including DNA replication, nucleotide excision repair and homologous recombination. Here, the role of RPA in the rejoining of radiation-induced DNA double-strand breaks (DSB) by non-homologous end-joining (NHEJ) was investigated. Methods and materials : A previously described in vitro assay for DSB rejoining was employed. The assay used 'naked' genomic DNA prepared from agarose-embedded G 1 -phase A549 cells as a substrate and extracts prepared from HeLa cells as a source of enzymes. Rejoining of DSB in this assay is absolutely dependent on cell extract and proceeds, under optimal reaction conditions, to an extent similar to that observed in intact cells. For experiments, extracts were supplemented with excess purified recombinant RPA. Alternatively, RPA was removed from the extracts either by fractionation or immunodepletion. Results : Although the rejoining of DSB in vitro was not absolutely dependent on RPA, it proceeded faster and to higher levels of completion when recombinant protein was added to the extracts. Depletion of RPA from extracts reduced the rejoining half-times and addition of purified recombinant protein restored the kinetics of DSB rejoining. Extract fractionation indicated the operation of at least two pathways in DSB rejoining, only one of which was facilitated by RPA. Conclusions : The results suggest that in addition to its role in homologous recombination, RPA may also have a supportive role in some forms of non-homologous end-joining.