UF, Princeton researchers unveil precision DNA editing breakthrough

• Recent advances in technology allow scientists to directly edit the genetic code in human DNA. 

• Piyush Jain, Ph.D., and a team of researchers have developed a new tool that promises more accurate and flexible genetic editing. 

• The tool is essentially a programmable “search and replace” tool for DNA. 

DNA is the body’s instruction manual. It contains the genetic code that tells cells how to grow, function and respond to the world.  

But like any code, DNA can contain mistakes. While some of these anomalies are harmless, others can contribute to inherited disorders, developmental problems or diseases like cancer. 

Researchers from the University of Florida and Princeton University have proposed a powerful new gene-editing technology that could transform the potential correction of genetic mutations, promising safer and more precise therapies for treating genetic diseases. 

Basically, the researchers have created a programmable “search-and-replace” tool for DNA. 

The new system, CODE — short for Chimeric Oligonucleotide-Directed Editing — was designed to make precise changes to DNA without cutting both strands of the genetic material, which can sometimes lead to unwanted errors.  

The CODE system is described in “Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing,” published recently in Nature Communications. Piyush Jain, Ph.D., an associate professor in the UF Department of Chemical Engineering, alongside Cameron Myhrvold, Ph.D., an assistant professor in the Department of Molecular Biology at Princeton University, led the project. 

Since 2012, scientists have used a technique known as CRISPR to edit DNA. Traditional CRISPR systems act a bit like molecular scissors: They cut the DNA, and then the cell tries to repair the break. The approach has proved to be successful, but it can lack precision, as the repair process can introduce new mistakes. 

Then came a major advance in gene editing known as prime editing, a method that allows scientists to rewrite DNA more carefully and without breaking both strands. Prime editing can swap a single DNA letter, insert small pieces of DNA or remove unwanted sections. While widely used by gene-editing scientists, prime editing proved to be effective only in certain spots in the genome. As a result, prime editing is somewhat limited in its application.  

The CODE system is a response to prime editing’s inherent limitations. 

CODE exploits a natural enzyme already present in the cells of many organisms, called DNA polymerase, to make editing even more precise, representing a further evolution in genetic editing.   

“With the CRISPR system, it’s only able to make a cut. With prime editing, we can make the repair, and CODE is now enabling a more efficient repair,” Jain explained.  

He likens prime editing to cutting a string with a pair of scissors, then adding a new desired piece with a pair of tweezers and gluing the strands back together. Prime’s limitation, continuing with the repair metaphor, is “sometimes everything gets glued, including the tweezer holding the string. It doesn’t know where to stop. That’s the problem. CODE has changed that.” 

The incorporation of DNA polymerase in place of the reverse transcriptase enzyme used by prime editing basically allows the editing system to know where in the DNA strand to stop the repair work, reducing unwanted edits and making greater precision possible. 

Although the CODE system is in the early stages of development, U.S. federal agencies, including the National Institutes of Health (NIH), the Food and Drug Administration (FDA) and ARPA-H, are actively accelerating the clinical translation of these next-generation gene-editing tools. Furthermore, there is a revival of excitement in the industry with these new developments. 

Researchers note that no single genetic editing tool works perfectly in all situations. Rather, CODE represents a new tool in the gene editor’s toolbox, a new class of genome-editing technology. The hope is that CODE will open the door to a broader family of editors built from DNA-copying enzymes found throughout nature. 

“Instead of relying on one standard editing platform, we are beginning to build custom toolkits from nature’s own molecular machinery.” 

Beyond experiments in human cells, the researchers were able to test CODE in mouse and bovine embryos. Results indicate that the system can function in more complex biological settings, not just in a controlled cell culture environment. According to Jain, demonstrating that this new platform can work in embryos is a major milestone, suggesting that DNA polymerase-based editors could eventually have applications in agriculture, developmental biology and — perhaps one day — therapeutic research. 

First authors of the paper, Long Nguyen and Noah Rakestraw, began the project while working together in Jain’s lab. After completing his doctorate, Nguyen joined Myhrvold’s lab as a post-doctoral researcher and continued working closely with Rakestraw on the project. The work was jointly supervised by Myhrvold and Jain and was completed with multiple collaborators across the two institutions. 

“It is incredibly rewarding to see the initiative of a former Ph.D. student, Long Nguyen, serve as the catalyst for this multi-institutional partnership as he continued to work closely with the co-first author, Noah Rakestraw, a current Ph.D. student in my lab,” Jain said. “This effort was made possible by Cameron Myhrvold’s unwavering support for what was then an unconventional collaboration, providing the foundation for our labs to turn this vision into a successful reality.” 

Myhrvold echoed the sentiment. “This has been a fantastic collaboration between Piyush Jain’s lab and my lab.”