Engineered enzyme enables fast and accurate RNA synthesis

From vaccines and diagnostics to emerging gene-based therapies, RNA molecules are now central to modern medicine. But as their use continues to grow, so does a fundamental challenge: producing RNA quickly, accurately and with the flexibility needed for next-generation biomedical applications.

Scientists at the University of California, Irvine have now taken a major step toward solving that problem.

In a study recently published in Nature Chemical Biology, a research team led by John Chaput, UC Irvine professor of pharmaceutical sciences, reports the creation of a powerful new enzyme that efficiently synthesizes RNA – something no natural DNA-copying enzyme can do. The engineered enzyme, known as C28, produces RNA at near-natural speeds while maintaining high accuracy and the ability to copy long sequences.

"DNA polymerases are naturally designed to reject RNA," Chaput said. "What surprised us is that we were able to overcome this barrier not by redesigning the enzyme's active site, but by letting evolution find unexpected structural solutions."

Rather than manually engineering the enzyme, the researchers turned to directed evolution. Using a high-throughput, single-cell screening platform, the team recombined related polymerase genes and tested millions of enzyme variants in parallel. After only a few rounds of selection, they identified C28 – a polymerase carrying dozens of mutations spread throughout the protein that collectively enable efficient RNA synthesis.

The result is an enzyme with unusual versatility. In addition to synthesizing RNA, C28 can perform reverse transcription, copying RNA back into DNA, and can generate hybrid DNA-RNA molecules using standard polymerase chain reaction techniques. The enzyme also readily accepts several chemically modified RNA building blocks, including those used in mRNA vaccines and RNA-based therapeutics.

This combination of speed, accuracy and flexibility could make C28 a valuable new tool for researchers and biotechnology developers, particularly in applications that require customized or chemically modified RNA molecules.

Beyond its practical applications, the research underscores the power of directed evolution to create entirely new molecular functions – capabilities that do not exist in nature but can be unlocked through carefully designed selection strategies.

"This work shows that enzymes are far more adaptable than we once thought," Chaput said. "By harnessing evolution, we can create new molecular tools that open the door to advances in RNA biology, synthetic biology and biomedical innovation."

Other UC Irvine team members were Esau Medina, Victoria Maola Gross, Mohammad Hajjar, Ethan Ho, Alexandria Horton, Nicholas Chim and Grace Ko. The National Science Foundation supported the research.