A team of researchers from the Arc Institute have discovered the bridge recombinase mechanism, a precise and powerful tool to recombine and rearrange DNA in a programmable way. Going far beyond programmable genetic scissors like CRISPR, the bridge recombinase mechanism enables scientists to specify not only the target DNA to be modified, but also the donor material to be recognized, so they can insert new, functional genetic material, cut out faulty DNA, or invert any two sequences of interest. Discover more in this short video visualizing the key aspects of the bridge recombination mechanism. Video created by Visual Science.
Palo Alto, CA, June 26, 2024 – Researchers from the Arc Institute have identified a novel mechanism called bridge recombinase, allowing for the recombination and rearrangement of DNA in a programmable manner. This mechanism, detailed in a study published in Nature, marks a significant advancement in genetic engineering, presenting the first DNA recombinase that employs a non-coding RNA for sequence-specific selection of target and donor DNA molecules.
"The bridge RNA system is a fundamentally new mechanism for biological programming," stated Hsu, the senior author of the study, an Arc Institute Core Investigator, and an Assistant Professor of Bioengineering at UC Berkeley. "Bridge recombination can universally modify genetic material through sequence-specific insertion, excision, inversion, and more, enabling a word processor for the living genome beyond CRISPR."
Origins and Mechanism
The bridge recombination system originates from insertion sequence 110 (IS110) elements, a type of transposable element or “jumping gene” that moves within and between microbial genomes. These elements have evolved as professional DNA manipulation machines to ensure their survival across various life forms. The IS110 elements consist solely of a gene encoding the recombinase enzyme and flanking DNA segments.
The Hsu lab discovered that when IS110 excises itself from a genome, the non-coding DNA ends join to produce an RNA molecule—the bridge RNA—which folds into two loops. One loop binds to the IS110 element itself, while the other binds to the target DNA. This bridge RNA represents the first bispecific guide molecule, determining the sequence of both target and donor DNA through base-pairing interactions.
Programmable RNA
Each loop of the bridge RNA is independently programmable, enabling researchers to pair any target and donor DNA sequences. This system extends beyond its natural role, allowing the insertion of any desirable genetic cargo into any genomic location. The team demonstrated over 60% insertion efficiency of a desired gene in E. coli with over 94% specificity for the correct genomic location.
“These programmable bridge RNAs distinguish IS110 from other known recombinases, which lack an RNA component and cannot be programmed,” said graduate student Nick Perry. “It’s as if the bridge RNA were a universal power adapter that makes IS110 compatible with any outlet.”
Structural Insights
The study's findings are bolstered by collaboration with Dr. Hiroshi Nishimasu’s lab at the University of Tokyo, which also published in Nature. The Nishimasu lab employed cryo-electron microscopy to determine the molecular structures of the recombinase-bridge RNA complex bound to target and donor DNA, sequentially illustrating the key steps of the recombination process.
With further exploration and development, the bridge mechanism could herald a third generation of RNA-guided systems, surpassing the DNA and RNA cutting mechanisms of CRISPR and RNA interference (RNAi). This unified mechanism for programmable DNA rearrangements addresses critical limitations of current genome editing technologies, notably joining both DNA strands without releasing cut DNA fragments.
Future Potential
“The bridge recombination mechanism solves some of the most fundamental challenges facing other methods of genome editing,” said research co-lead Matthew Durrant. “The ability to programmably rearrange any two DNA molecules opens the door to breakthroughs in genome design.”
Publication Details
Durrant, M.G., Perry, N.T., Pai, J.J. et al. Bridge RNAs direct programmable recombination of target and donor DNA. Nature 630, 984–993 (2024). https://doi.org/10.1038/s41586-024-07552-4
Hiraizumi, M., Perry, N.T., Durrant, M.G. et al. Structural mechanism of bridge RNA-guided recombination. Nature 630, 994–1002 (2024). https://doi.org/10.1038/s41586-024-07570-2