The atomic coordinates of LcDdmD-fork DNA, LcDdmE-gDNA-bubbleDNA, and LcDdmDE-guide-bubbleDNA have been deposited in the RCSB PDB under accession numbers 9IX4, 9IW3 and 9IXM, respectively, and the corresponding cryo-EM maps have also been deposited in the EMDB under accession numbers EMD-60964, EMD-60944, and EMD-60973, respectively.