Figure 1. (a) Schematic of the recombination core sites of a serine and tyrosine recombinase (not to scale). The 2-bp and 6–8-bp central (overlap) regions lie between the sites of recombinase-mediated cleavage (arrows). Recombinase molecules are depicted as ovoids containing their respective nucleophiles. (b) Organization of the bacteriophage attP and attB recombination sites. Recombinase-binding sites are indicated by arrows (solid lines for core binding and dashed lines for binding to the accessory sequence arms P and P¢; different regions of the recombinases contact these different types of site). Binding sites for the accessory proteins IHF, FIS and Xis are also indicated. Recombination between attP and attB generates attL (P¢ plus core) and attR (P plus core).

Figure 2. Outcomes of site-specific recombination.

Figure 3. Role of accessory sequences and proteins in resolution and inversion selectivity. (a) The recombination site for Tn3 and resolvase contains a core site (site I) and two adjacent accessory sites (sites II and III). All three sites bind two molecules of resolvase. Recombination occurs at site I, and resolvase bound at sites II and III acts as an accessory protein that entraps three plectonemic supercoils. Intramolecular recombination between two directly repeated (DR) sites forms a –2 catenane recombinant product. The specific geometry of the synapse restricts recombination to intramolecular events between directly repeated molecules. (b) Schematic of synapsed directly repeated (DR) cer sites, the substrate for recombination by XerCD. In this case the accessory sequences (AS) are bound by ArgR and PepA. A –4 catenane results from recombination. In reality, the recombination sites may synapse in a close to antiparallel orientation, making an extra node entrapped between the recombination sites in addition to the three shown. (c) Schematic of synapsed inverted (IR) gix sites, the substrate for Gin invertase. Binding of the accessory protein, FIS to a distant enhancer site (E), entraps two negative supercoils, and thereby ensures inversion selectivity.

Figure 4. (a) Reaction pathway for serine recombinases. (b) Reaction pathway for tyrosine recombinases. (c) Chemistry of serine recombinase-mediated site-specific recombination. (d) Chemistry of tyrosine recombinase-mediated site-specific recombination.

Figure 5. Three strategies for Hin, Gin and Fim invertase-mediated gene switches. Inverted recombination sites are shown as horizontal arrows. Promoters and their transcripts are shown by p (promoter) followed by a zig-zag line indicating the transcript.