The article reports the discovery of a novel mechanism for programmable DNA recombination using IS110 insertion sequences, a family of minimal and autonomous mobile genetic elements. The authors identify a structured non-coding RNA (ncRNA) that binds specifically to the encoded recombinase, facilitating sequence-specific recombination between target and donor DNA molecules. This ncRNA, termed the "bridge RNA," contains two internal loops that base-pair with the target DNA and the donor DNA, which is the IS110 element itself. The study demonstrates that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination, enabling insertion, excision, and inversion of DNA molecules. The modular nature of the bridge RNA allows for the design of diverse recombination events, including the insertion of DNA into specific genomic sites and the programmable excision and inversion of DNA sequences. The IS110 bridge recombination system expands the diversity of nucleic-acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design. The authors also investigate the evolutionary conservation and diversity of the bridge RNA across different IS110 subfamilies, highlighting its potential for further functional insights and applications in genome engineering.The article reports the discovery of a novel mechanism for programmable DNA recombination using IS110 insertion sequences, a family of minimal and autonomous mobile genetic elements. The authors identify a structured non-coding RNA (ncRNA) that binds specifically to the encoded recombinase, facilitating sequence-specific recombination between target and donor DNA molecules. This ncRNA, termed the "bridge RNA," contains two internal loops that base-pair with the target DNA and the donor DNA, which is the IS110 element itself. The study demonstrates that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination, enabling insertion, excision, and inversion of DNA molecules. The modular nature of the bridge RNA allows for the design of diverse recombination events, including the insertion of DNA into specific genomic sites and the programmable excision and inversion of DNA sequences. The IS110 bridge recombination system expands the diversity of nucleic-acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design. The authors also investigate the evolutionary conservation and diversity of the bridge RNA across different IS110 subfamilies, highlighting its potential for further functional insights and applications in genome engineering.