Fig. 1. Topology of site-specific recombination reactions. (A) Xer recombination at psi occurs only after the formation of a synaptic complex with a defined local structure (shown boxed). This productive synapse, formed by wrapping the accessory sequences of two recombination sites around the accessory protein PepA, traps a specific number of topological nodes. Strand exchange occurs by a defined mechanism and the product is a right-handed four-noded catenane with antiparallel psi sites. (B) Many site-specific recombination systems display no topological specificity. A random number of supercoils are trapped when the recombination sites come together, and recombination generates products of mixed topology. Sites in direct repeat yield two circles, which are either unlinked, or linked in catenanes with even numbers of topological crossings or nodes, as shown. Sites in an inverted repeat yield single circular products, which are either unknotted or knotted with an odd number of nodes. Knots and catenanes produced in these reactions are generally members of the torus family of knots and catenanes, as shown.