In medicine and biotechnology, the power to evolve proteins with recent or improved functions is crucial, but current methods are sometimes slow and laborious. Now, Scripps Research scientists have developed an artificial biology platform that accelerates evolution itself — enabling researchers to evolve proteins with useful, recent properties 1000’s of times faster than nature. The system, named T7-ORACLE, was described in Science on August 7, 2025, and represents a breakthrough in how researchers can engineer therapeutic proteins for cancer, neurodegeneration and essentially every other disease area.
“That is like giving evolution a fast-forward button,” says co-senior writer Pete Schultz, the President and CEO of Scripps Research, where he also holds the L.S. “Sam” Skaggs Presidential Chair. “You possibly can now evolve proteins repeatedly and precisely inside cells without damaging the cell’s genome or requiring labor-intensive steps.”
Directed evolution is a laboratory process that involves introducing mutations and choosing variants with improved function over multiple cycles. It’s used to tailor proteins with desired properties, resembling highly selective, high-affinity antibodies, enzymes with recent specificities or catalytic properties, or to analyze the emergence of resistance mutations in drug targets. Nevertheless, traditional methods often require repeated rounds of DNA manipulation and testing with each round taking per week or more. Systems for continuous evolution — where proteins evolve inside living cells without manual intervention — aim to streamline this process by enabling simultaneous mutation and selection with each round of cell division (roughly 20 minutes for bacteria). But existing approaches have been limited by technical complexity or modest mutation rates.
T7-ORACLE circumvents these bottlenecks by engineering E. coli bacteria — a regular model organism in molecular biology — to host a second, artificial DNA replication system derived from bacteriophage T7, a virus that infects bacteria and has been widely studied for its easy, efficient replication system. T7-ORACLE enables continuous hypermutation and accelerated evolution of biomacromolecules, and is designed to be broadly applicable to many protein targets and biological challenges. Conceptually, T7-ORACLE builds on and extends efforts on existing orthogonal replication systems — meaning they operate individually from the cell’s own machinery — resembling OrthoRep in Saccharomyces cerevisiae (baker’s yeast) and EcORep in E. coli. Compared to those systems, T7-ORACLE advantages from the mix of high mutagenesis, fast growth, high transformation efficiency, and the benefit with which each the E. coli host and the circular replicon plasmid will be integrated into standard molecular biology workflows.
The T-7 ORACLE orthogonal system targets only plasmid DNA (small, circular pieces of genetic material), leaving the cell’s host genome untouched. By engineering T7 DNA polymerase (a viral enzyme that replicates DNA) to be error-prone, the researchers introduced mutations into goal genes at a rate 100,000 times higher than normal without damaging the host cells.
“This method represents a significant advance in continuous evolution,” says co-senior writer Christian Diercks, an assistant professor of chemistry at Scripps Research. “As an alternative of 1 round of evolution per week, you get a round every time the cell divides — so it really accelerates the method.”
To exhibit the ability of T7-ORACLE, the research team inserted a typical antibiotic resistance gene, TEM-1 β-lactamase, into the system and exposed the E. coli cells to escalating doses of assorted antibiotics. In lower than per week, the system evolved versions of the enzyme that would resist antibiotic levels as much as 5,000 times higher than the unique. This proof-of-concept demonstrated not only T7-ORACLE’s speed and precision, but additionally its real-world relevance by replicating how resistance develops in response to antibiotics.
“The surprising part was how closely the mutations we saw matched real-world resistance mutations present in clinical settings,” notes Diercks. “In some cases, we saw recent mixtures that worked even higher than those you’ll see in a clinic.”
But Diercks emphasizes that the study is not focused on antibiotic resistance per se.
“This is not a paper about TEM-1 β-lactamase,” he explains. “That gene was only a well-characterized benchmark to point out how the system works. What matters is that we will now evolve virtually any protein, like cancer drug targets and therapeutic enzymes, in days as an alternative of months.”
The broader potential of T7-ORACLE lies in its adaptability as a platform for protein engineering. Although the system is built into E. coli, the bacterium serves primarily as a vessel for continuous evolution. Scientists can insert genes from humans, viruses or other sources into plasmids, that are then introduced into E. coli cells. T7-ORACLE mutates these genes, generating variant proteins that will be screened or chosen for improved function. Because E. coli is simple to grow and widely utilized in labs, it provides a convenient, scalable system for evolving virtually any protein of interest.
This might help scientists more rapidly evolve antibodies to focus on specific cancers, evolve simpler therapeutic enzymes, and design proteases that focus on proteins involved in cancer and neurodegenerative disease.
“What’s exciting is that it is not limited to 1 disease or one type of protein,” says Diercks. “Since the system is customizable, you may drop in any gene and evolve it toward whatever function you wish.”
Furthermore, T7-ORACLE works with standard E. coli cultures and widely used lab workflows, avoiding the complex protocols required by other continuous evolution systems.
“The most important thing that sets this apart is how easy it’s to implement,” adds Diercks. “There isn’t any specialized equipment or expertise required. When you already work with E. coli, you may probably use this technique with minimal adjustments.”
T7-ORACLE reflects Schultz’s broader goal: to rebuild key biological processes — resembling DNA replication, RNA transcription and protein translation — in order that they function independently of the host cell. This separation allows scientists to reprogram these processes without disrupting normal cellular activity. By decoupling fundamental processes from the genome, tools like T7-ORACLE help advance synthetic biology.
“In the long run, we’re fascinated with using this technique to evolve polymerases that may replicate entirely unnatural nucleic acids: synthetic molecules that resemble DNA and RNA but with novel chemical properties,” says Diercks. “That might open up possibilities in synthetic genomics that we’re just starting to explore.”
Currently, the research team is concentrated on evolving human-derived enzymes for therapeutic use, and on tailoring proteases to acknowledge specific cancer-related protein sequences.
“The T7-ORACLE approach merges the most effective of each worlds,” says Schultz. “We are able to now mix rational protein design with continuous evolution to find functional molecules more efficiently than ever.”
Along with Diercks and Schultz, authors of the study, “An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli,” are Philipp Sondermann, Cynthia Rong, Thomas G. Gillis, Yahui Ban, Celine Wang and David A. Dik of Scripps Research.
This work was supported by funding from the National Institutes of Health (grant RGM145323A).