The formation of triple-stranded DNA prevents spontaneous branch-migration

Branch-migration is a fundamental step in the process of DNA recombination that determines the location, and extent, of the exchange between the recombining duplexes. Four-way Holliday junctions assembled in vitro can migrate spontaneously in an uncatalysed reaction that mimics some of the aspects involved in branch-migration. Here, we have analysed the effects of a d(GA . TC)(22) and a d(CA . TG)(30) sequence on the rate of spontaneous branch-migration. Under most of the experimental conditions assayed, no significant effect was observed. However, the d(GA . TC)(22) sequence induces a very strong arrest when branch-migration is performed at low pH, under conditions where the repeated sequence is forming an intramolecular [C+T(GA . TC)] triplex. A similar arrest is observed when the recombining duplexes contain intermolecular triplexes arising from the annealing of a d(GA . TC)(22) duplex and a d(TC)(22) oligonucleotide, indicating that the formation of tripler DNA constitutes a strong barrier for the progression of the Holliday junction. These results are discussed in the context of the possible contribution of tripler DNA to DNA recombination. (C) 1999 Academic Press.