Improved method for the generation of double Holliday junction DNAs

Recombinational repair provides an important pathway for the repair of DNA double strand breaks that arise in mitotic and meiotic cells. Homologous pairing and strand exchange leads to the formation of DNA intermediates that are linked by double Holliday junctions, and these need to be resolved prior to chromosome segregation and cell division. In mitotic cells, resolution occurs by either of two distinct pathways (i) Nucleolytic cleavage by GEN1 or SLX1-SLX4-MUS81-EME1-XPF-ERCC1 (SMX complex), or (ii) dissolution mediated by BLM-TopoIIIα-RMI1-RMI2 (BTRR complex). To facilitate the biochemical analysis of these pathways, we previously developed a novel methodology, involving DNAzyme self-cleavage, to generate 1.8-kb long DNA molecules containing dHJs. This involved the sequential annealing of precursor ssDNAs, which were first individually isolated through multiple rounds of gel purification and ethanol precipitation, but unfortunately the method was laborious and inefficient as considerable DNA losses were incurred at each step. Here, we describe a significantly improved methodology, that increases both the efficiency and yield without impacting the quality of the dHJs produced. The new method is rapid and simple, requiring only basic molecular biology expertise, and results in the formation of dHJs that make ideal substrates for the biochemical analysis of dissolution and resolution reaction in vitro.