Fig. 4: Strand exchange mechanism.

a–i, Schematics of TBL–tDNA and DBL–dDNA and the structures of tDNA and dDNA, and TBL–tDNA and DBL–dDNA, in the IS621 synaptic complexes in the pre-strand exchange state (the complex with the WT bRNA for comparison) (a–c); the post-strand exchange, Holliday junction intermediate state (state 1) (d–f); and the post-strand exchange, Holliday junction resolution state (state 2) (g–i). DNA cleavage sites are indicated by yellow triangles, whereas partial cleavage and religation are indicated by green triangles. In b,e,h, cryo-EM density maps are shown as grey semi-transparent surfaces. In b,c, disordered regions are indicated by dotted lines. In c,f,i, positions 6–9 in the dDNA and tDNA are numbered.