title: Preferential synapsis of loxP sites drives ordered strand exchange in Cre-loxP site-specific recombination.
abstract: The bacteriophage P1 Cre recombinase catalyzes site-specific recombination between 34-base-pair loxP sequences in a variety of topological contexts. This reaction is widely used to manipulate DNA molecules in applications ranging from benchtop cloning to genome modifications in transgenic animals. Despite the simple, highly symmetric nature of the Cre-loxP system, there is strong evidence that the reaction is asymmetric; the 'bottom' strands in the recombining loxP sites are preferentially exchanged before the 'top' strands. Here, we address the mechanistic basis for ordered strand exchange in the Cre-loxP recombination pathway. Using suicide substrates containing 5'-bridging phosphorothioate linkages at both cleavage sites, fluorescence resonance energy transfer between synapsed loxP sites and a Cre mutant that can cleave the bridging phosphorothioate linkage but not a normal phosphodiester linkage, we showed that preferential formation of a specific synaptic complex between loxP sites imposes ordered strand exchange during recombination and that synapsis stimulates cleavage of loxP sites.
authors.affiliation: Department of Biochemistry & Biophysics and Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Kaushik
authors.initials: K
authors.lastname: Ghosh
authors.forename: Chi-Kong
authors.initials: CK
authors.lastname: Lau
authors.forename: Kushol
authors.initials: K
authors.lastname: Gupta
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Van Duyne
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D023902:Chromosome Pairing; D004254:DNA Nucleotidyltransferases / Q000235:genetics; D031541:Fluorescence Resonance Energy Transfer; D019426:Integrases / Q000235:genetics*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011995:Recombination, Genetic; D015398:Signal Transduction; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D014764:Viral Proteins; C045073:Cre recombinase; D004254:DNA Nucleotidyltransferases; D019426:Integrases; C077570:Site-specific recombinase