If not properly processed and repaired, DNA double-strand breaks (DSBs) can give rise to deleterious chromosome rearrangements, which could ultimately lead to the tumor phenotype 1, 2. DSB ends are resected in a 5′ to 3′ fashion in cells, to yield single-stranded DNA for the recruitment of factors critical for DNA damage checkpoint activation and repair by homologous recombination2. The resection process involves redundant pathways consisting of nucleases, DNA helicases, and associated proteins3. Being guided by recent genetic studies 4-6 , we have reconstituted the first eukaryotic ATP-dependent DNA end resection machinery comprising the Saccharomyces cerevisiae Mre11-Rad50-Xrs2 (MRX) complex, the Sgs1-Top3-Rmi1 (STR) complex, Dna2 protein and the heterotrimeric single-strand DNA binding protein RPA. We show that DNA strand separation during end resection is mediated by the Sgs1 helicase function, in a manner that is enhanced by Top3-Rmi1 and MRX. In congruence with genetic observations 6 , while the Dna2 nuclease activity is critical for resection, the Mre11 nuclease activity is dispensable. By examining the top3 Y356F allele and its encoded protein, we provide evidence that the topoisomerase activity of Top3, although critical for the suppression of crossover recombination 2,7 , is not needed for resection either in cells or in the reconstituted system. Our results also unveil a multi-faceted role of RPA, in the sequestration of ssDNA generated by DNA unwinding, enhancement of 5′ strand incision, and protection of the 3′ strand. Our reconstituted system should serve as a useful model for delineating the mechanistic intricacy of the DNA break resection process in eukaryotes.The 3′ ssDNA strands derived from DSB resection attract RPA, which promotes the recruitment of checkpoint proteins to effect cell cycle arrest 8 . With the aid of a recombination mediator protein, such as yeast Rad52 or human BRCA2, the Rad51 recombinase displaces RPA from the ssDNA to assemble into a right-handed helical polymer capable of initiating DSB repair by homologous recombination 1,2 . Genetic studies in yeast have shown that DSB resection proceeds in two steps. The MRX complex plays a 3 To whom correspondences and request for materials should be addressed: Gregory Ira: gira@bcm.edu, Patrick Sung: patrick.sung@yale.edu. role in initiation, while the Sgs1 helicase, its associated proteins Top3 and Rmi1, and the helicase/nuclease Dna2, whose nuclease activity is needed for Okazaki fragment processing 9,10 , constitute the DNA motor-driven path of long-range resection. Exo1, a 5′-3′ exonuclease, defines a redundant resection means 4-6 . Here we reconstitute the Sgs1/Dna2-dependent DNA resection machinery and present results germane for understanding its mechanistic underpinnings.The requisite factors, namely, Sgs1, Top3-Rmi1 (TR) complex, MRX complex, Dna2, and RPA were purified and analyzed (see Supplementary Fig. 2 and the Supplementary Information). As shown in Figure 1a, the combination of these factors degraded a 1.9-kb ...

During DNA repair by homologous recombination (HR), DNA synthesis copies information from a template DNA molecule. Multiple DNA polymerases have been implicated in repair-specific DNA synthesis1–3, but it has remained unclear whether a DNA helicase is involved in this reaction. A good candidate is Pif1, an evolutionarily conserved helicase in S. cerevisiae important for break-induced replication (BIR)4 as well as HR-dependent telomere maintenance in the absence of telomerase5 found in 10–15% of all cancers6. Pif1 plays a role in DNA synthesis across hard-to-replicate sites7, 8 and in lagging strand synthesis with Polδ9–11. Here we provide evidence that Pif1 stimulates DNA synthesis during BIR and crossover recombination. The initial steps of BIR occur normally in Pif1-deficient cells, but Polδ recruitment and DNA synthesis are decreased, resulting in premature resolution of DNA intermediates into half crossovers. Purified Pif1 protein strongly stimulates Polδ-mediated DNA synthesis from a D-loop made by the Rad51 recombinase. Importantly, Pif1 liberates the newly synthesized strand to prevent the accumulation of topological constraint and to facilitate extensive DNA synthesis via the establishment of a migrating D-loop structure. Our results uncover a novel function of Pif1 and provide insights into the mechanism of HR.

Summary Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair ssDNA with a homologous dsDNA template. Here we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real-time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a 9th nucleotide coincides with an additional reduction in binding free energy and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination.

The tumor suppressor complex BRCA1-BARD1 functions in DNA double-strand break repair by homologous recombination. Therein, BRCA1-BARD1 facilitates the nucleolytic resection of DNA ends to generate a single-stranded template for the recruitment of another tumor suppressor complex BRCA2-PALB2 and the recombinase RAD51. By examining purified BRCA1-BARD1 and mutants, we show that BRCA1 and BARD1 both bind DNA and interact with RAD51, and that BRCA1-BARD1 enhances the recombinase activity of RAD51. Mechanistically, BRCA1-BARD1 promotes the assembly of the synaptic complex, an essential intermediate in RAD51-mediated DNA joint formation. Evidence is provided that BRCA1 and BARD1 are both indispensable for RAD51 stimulation. Importantly, BRCA1-BARD1 mutants weakened for RAD51 interaction are compromised for DNA joint formation and for the mediation of homologous recombination and DNA repair in cells. Our results identify a late role of BRCA1-BARD1 in homologous recombination, a novel attribute of the tumor suppressor complex that could be targeted in cancer therapy.

Glutathione (GSH) plays a crucial role in human pathologies. Near-infrared fluorescence-based sensors capable of detecting intracellular GSH in vivo would be useful tools to understand the mechanisms of diseases. In this work, two cyanine-based fluorescent probes, 1 and 2, containing sulfonamide groups were prepared. Evaluation of the fluorescence changes displayed by probe 1, which contains a 2,4-dinitrobenzenesulfonamide group, shows that it is cell-membrane-permeable and can selectively detect thiols such as GSH, cysteine (Cys), and homocysteine (Hcy) in living cells. The response of 1 to thiols can be reversed by treatment with N-methylmaleimide (NMM). Probe 2, which possesses a 5-(dimethylamino)naphthalenesulfonamide group, displays high selectivity for GSH over Cys and Hcy, and its response can be reversed using NMM. The potential biological utility of 2 was shown by its use in fluorescence imaging of GSH in living cells. Furthermore, probe 2 can determine changes in the intracellular levels of GSH modualated by H2O2. The properties of 2 enable its use in monitoring GSH in vivo in a mouse model. The results showed that intravenous injection of 2 into a mouse generates a dramatic image in which strong fluorescence is emitted from various tissues, including the liver, kidney, lung, and spleen. Importantly, 2 can be utilized to monitor the depletion of GSH in mouse tissue cells promoted by excessive administration of the painkiller acetaminophen. The combined results coming from this effort suggest that the new probe will serve as an efficient tool for detecting cellular GSH in animals.