Single Molecule Experiments Define the Role of Nbs1 and Xrs2 in DNA Tethering by MRN and MRX in DSB Repair

Abstract

To ensure genome stability and hinder introduction of disease-causing changes, DNA double-strand breaks (DSB) need to be repaired. Homologous recombination (HR) is a key DSB repair pathway. At the start of HR, the MRE11-RAD50-NBS1 (MRN) complex finds the broken ends and upon stimulation of its nuclease activity by CtIP performs the DSB processing for repair. The repair process involves DNA tethering, which is poorly understood. in this study, we use single-molecule analysis to investigate how MRN interacts with long DNA. The method is based on confining long DNA molecules in nanochannels. in contrast to tethering one or both ends to a substrate, as in most common single DNA molecule methods, the DNA is completely free in the nano channels, meaning that reaction on the DNA ends can be studied. Single molecule experiments with MRN and DNA in nanochannels show direct evidence of a strong DNA interaction and tethering of distant DNA fragments by MRN. When comparing MRN and the yeast homologue Mre11-Rad50-Xrs2 (MRX), we observed key similarities. in both systems, the absence of NBS1/Xrs2, lowers the concatemer and circle formation dramatically. Data from single molecule experiments and EMSA show that NBS1 and Xrs2 alone have a strong DNA interaction. These findings strengthen the theory of Nbs1/Xrs2 playing a role in the localization of the MRN/X complex to DNA ends and mediate DNA annealing. Finally, the addition of the MRN/X co-factor CtIP and Sae2, respectively, shows little to no effect on the bridging by MRN/X, although both CtIP and Sae2 exhibit strong DNA bridging on their own. Thus the interaction between MRN/X and the co-factor that is crucial for the nuclease activity is potentially not important for DNA bridging.