Bridge recombinases, optimized for human cells, enable massive programmable DNA rearrangements

(Press-News.org) For decades, gene-editing science has been limited to making small, precise edits to human DNA, akin to correcting typos in the genetic code. Arc Institute researchers are changing that paradigm with a universal gene editing system that allows for cutting and pasting of entire genomic paragraphs, rearranging whole chapters, and even restructuring entire passages of the genomic manuscript.

In a paper published September 25, 2025 in the journal Science, the research team shows how bridge recombinase technology can be applied to human cells. The advance allows scientists to manipulate large genomic regions, testing up to a million base pairs in length, by inserting new genes, deleting entire gene clusters, or inverting regulatory sequences.

“Bridge recombinases could transform how we create genetic therapies by offering one versatile medicine per patient population instead of thousands of individual treatments,” says senior author Patrick Hsu (x: @pdhsu), an Arc Institute Core Investigator and University of California, Berkeley bioengineering faculty member. “With the ability to move and reshape entire genetic regions, we can engineer biology at the scale that evolution operates upon and apply those capabilities to solving complex diseases.”

Bridge recombinases were discovered from parasitic mobile genetic elements that hijack bacterial genomes for their own survival. Presented last year in the journal Nature, the same team found these elements encode both a new class of structured guide RNA, which they named a "bridge RNA", and a recombinase enzyme that rearranges DNA. Hsu and his colleagues repurposed this natural system by reprogramming the bridge RNA to target new DNA sequences, creating the foundation for a new type of precise gene editing tool they called bridge recombinases.

“What's different about our new paper is not only are we able to show insertion into the human genome but we're also showing quite efficiently the excision and inversion of genomic sequences in a programmable way,” says lead author Nicholas Perry (x: @ntperry13), an Arc scientist in the Hsu Lab who also conducted this research as a UC Berkeley PhD student. “The applications of this platform are particularly exciting and could apply broadly across many kinds of scientific projects.”

Starting with 72 different natural bridge recombinase systems isolated from bacteria, the team found that about 25% showed some activity in human cells, but most were barely detectable. Only one system, called ISCro4, showed enough measurable activity to enable further optimization. They then systematically improved both the protein and its RNA guide components, testing thousands of variations until they achieved 20% efficiency for DNA insertions and 82% specificity for hitting intended targets in the human genome.

While CRISPR uses a single guide RNA to target one DNA location, bridge RNAs are unique because they can simultaneously recognize two different DNA targets through distinct binding loops. This dual recognition enables the system to perform coordinated rearrangements such as bringing together distant chromosomal regions to excise genetic material or flipping existing sequences in reverse orientation. The system acts as molecular scaffolding that holds two DNA sites together while the recombinase enzyme performs the rearrangement reaction.

As a proof-of-concept, the researchers created artificial DNA constructs containing the same toxic repeat sequences that cause progressive neuromuscular decline in Friedreich's ataxia patients. While healthy individuals carry fewer than 10 sequential copies of a three-letter DNA sequence, people with the disorder can harbor up to 1,700 copies, which interferes with normal gene function. The engineered ISCro4 successfully removed these repeats from the artificial constructs, in some cases eliminating over 80% of the expanded sequences.

“Since disease severity correlates with repeat length, any amount of excision, whether it's a perfectly healthy genotype or not, has the potential to improve patient symptoms," Perry says. “Bridge recombinases could apply to any heritable disease that result from expansions, and because we only need to deliver RNA molecules rather than proteins or DNA to make it work inside human cells, the approach could be much simpler to implement and scale.”

The team also demonstrated that bridge recombinases could replicate existing therapeutic approaches by successfully removing the BCL11A enhancer, the same target disrupted in an FDA-approved sickle cell anemia treatment. And because bridge recombinases can move massive amounts of DNA, the technology could also help model the large-scale genomic rearrangements associated with cancers.

The investigators are now working to expand the platform's capabilities, including testing bridge recombinases in clinically relevant immune cells and stem cells, developing therapeutic delivery methods, and engineering variants that can handle DNA segments larger than a million base pairs. They also plan to explore applications in plant genetics and synthetic biology.

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The study represents a collaborative effort across multiple research teams. In addition to Nicholas Perry, key contributors included Liam Bartie, Dhruva Katrekar, Gabriel Gonzalez, and Matthew Durrant. The research was co-led by Patrick Hsu and Silvana Konermann at Arc Institute and Stanford University, with structural and mechanistic insights from Hiroshi Nishimasu at the University of Tokyo. Funding information and declarations of interest can be found in the published paper.

Perry, N. T., Bartie, L. J., Katrekar, D., Gonzalez, G. A., Durrant, M. G., Pai, J. J., Fanton, A., Martins, J. Q., Hiraizumi, M., Ricci-Tam, C., Nishimasu, H., Konermann, S., & Hsu, P. D. (2025). Megabase-scale human genome rearrangement with programmable bridge recombinases. Science. DOI: 10.1126/science.adz0276

Arc Institute (x: @arcinstitute) is an independent nonprofit research organization located in Palo Alto, California, that aims to accelerate scientific progress and understand the root causes of complex diseases. Arc's model gives scientists complete freedom to pursue curiosity-driven research agendas and fosters deep interdisciplinary collaboration. The Institute operates in close partnership with Stanford University, the University of California, Berkeley, and the University of California, San Francisco.

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