Analyzing the branch migration activities of eukaryotic proteins

The Holliday junction is a key intermediate of DNA repair, recombination, and replication. Branch migration of Holliday junctions is a process in which one DNA strand is progressively exchanged for another. Branch migration of Holliday junctions may serve several important functions such as affecting the length of genetic information transferred between homologous chromosomes during meiosis, restarting stalled replication forks, and ensuring the faithful repair of double strand DNA breaks by homologous recombination. Several proteins that promote branch migration of Holliday junctions have been recently identified. These proteins, which function during DNA replication and repair, possess the ability to bind Holliday junctions and other branched DNA structures and drive their branch migration by translocating along DNA in an ATPase-dependent manner. Here, we describe methods employing a wide range of DNA substrates for studying proteins that catalyze branch migration of Holliday junctions.