Fig. 5: Bridge recombination mechanism.

a,b, Proposed mechanisms of the IS621 synaptic complex formation (a) and the IS621-mediated DNA recombination (b). Two IS621 recombinase molecules bind to the TBL and DBL from two different bRNA molecules to form the IS621–TBL and IS621–DBL dimeric complexes, respectively. IS621–TBL and IS621–DBL recognize tDNA and dDNA, respectively, and then IS621–TBL–tDNA and IS621–DBL–dDNA form the tetrameric synaptic complex. In the synaptic complex, the top strands of tDNA and dDNA are cleaved at the RuvC–Tnp active sites, with the catalytic S241 residues forming covalent 5′-phosphoserine intermediates. The top strands are then exchanged and religated to form a Holliday junction (HJ) intermediate, which is resolved by the cleavage of the bottom strands at the RuvC–Tnp active sites. It is possible that the bottom strands are exchanged, and mismatched nucleotides are excised and repaired in E. coli cells, thereby completing the recombination. DNA cleavage sites are indicated by yellow triangles. Canonical and non-canonical base pairs are indicated by grey and red lines, respectively.