title: Interactions of protein complexes on supercoiled DNA: the mechanism of selective synapsis by Tn3 resolvase.
abstract: "Looping" interactions of distant sites on DNA molecules, mediated by DNA-binding proteins, feature in many regulated genetic processes. We used plasmids containing up to six res recombination sites for Tn3 resolvase to analyse looping interactions (synapsis) in this system. We observed that in plasmids with four or more res sites, certain pairs of sites recombine faster than others. The relative rates of recombination depend on the number, relative orientation, and arrangement of the sites. To account for the differences in rate, we propose that pairing interactions between resolvase-bound res sites are in a state of rapid flux, leading to configurations in which the maximum number of sites within each supercoiled substrate molecule are synapsed in a topologically simple arrangement. Recombination rates reflect the steady state concentrations of these synapse configurations. Our results are at variance with models for selective synapsis that rely on ordered motions within supercoiled DNA, "slithering" or "tracking", but are compatible with models that call for reversible synapsis of pairs of sites by random collision, followed by formation of an interwound productive synapse.
authors.affiliation: Institute of Biomedical and Life Sciences, University of Glasgow, 56 Dumbarton Road, Glasgow G11 6NU, Scotland, UK.
authors.forename: J Lesley
authors.initials: JL
authors.lastname: Brown
authors.forename: Jiuya
authors.initials: J
authors.lastname: He
authors.forename: David J
authors.initials: DJ
authors.lastname: Sherratt
authors.forename: W Marshall
authors.initials: WM
authors.lastname: Stark
authors.forename: Martin R
authors.initials: MR
authors.lastname: Boocock
mesh_terms: D001665:Binding Sites; D004251:DNA Transposable Elements / Q000235:genetics; D004278:DNA, Superhelical / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D045522:Recombinases; D011995:Recombination, Genetic / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D013379:Substrate Specificity; D019895:Transposases / Q000378:metabolism*; D045564:Transposon Resolvases
chemical_list: D004251:DNA Transposable Elements; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D045522:Recombinases; C473491:Tn3 resolvase; D019895:Transposases; D045564:Transposon Resolvases