title: Sensing homology at the strand-swapping step in lambda excisive recombination.
abstract: lambda Site-specific recombination requires a short stretch of sequence homology that might be sensed during strand swapping, during ligation and/or during isomerization of the obligate Holliday junction intermediate. Here, we use half-att site suicide substrates to study single and double top-strand-transfers, isolated from the subsequent steps of the reaction. The double-strand-transfer is analogous to a top-strand exchange and consists of one normal top-strand and one "contrary" bottom-strand to top-strand ligation between the half-att site substrate and its full-site partner. The resulting covalent three-way DNA junctions are poor substrates for resolution in the forward or reverse direction. We show that both the rate and the efficiency of Y-junction formation are homology dependent. Pairing of three nucleotides (either in the forward or in the contrary alignment) provides maximal stability to strand swapping. Complementary base-pairing next to one top-strand site (with or without ligation) stimulates strand-transfer at the other mismatched site. The data suggest that homology can be sensed at the strand-swapping step before ligation. However, homology also stimulates ligation and stabilizes the products, as is evident from the different rates of closed Y-junction formation in the presence or absence of homology. Furthermore, under recombination conditions, single top-strand-transfers are subject to reversal even in the presence of sequence homology; stability depends on a double-strand-transfer, i.e. dissociation of covalent Int.
authors.affiliation: Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
authors.forename: S E
authors.initials: SE
authors.lastname: Nunes-Düby
authors.forename: D
authors.initials: D
authors.lastname: Yu
authors.forename: A
authors.initials: A
authors.lastname: Landy
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D010582:Bacteriophage lambda / Q000235:genetics*; D004279:DNA, Viral / Q000378:metabolism; D019426:Integrases / Q000378:metabolism; D008565:Membrane Proteins / Q000378:metabolism; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid
chemical_list: C108089:AttR protein, bacteria; D001426:Bacterial Proteins; D004279:DNA, Viral; D008565:Membrane Proteins; D019426:Integrases