Researchers at the University of California at Irvine have developed a DNA enzyme, or DNAzyme, that can distinguish between two RNA strands within a cell and cut the disease-associated strand while leaving the healthy strand intact. This innovative “gene silencing” technology could revolutionize the development of DNAzymes to treat cancer, infectious diseases and neurological disorders.
DNAzymes are nucleic acid enzymes that cut other molecules. Through chemistry, the UCI team developed the enzyme Dz 46, which specifically targets the allele-specific RNA mutation in the KRAS gene, the major regulator of cell growth and division, found in 25 percent percent of all human cancers. A description of how the team achieved the evolution of this enzyme was recently published in the online journal Nature Communications.
“Generating DNAzymes that can function effectively in the natural conditions of cellular systems has been more challenging than expected,” said corresponding author John Chaput, a UCI professor of pharmaceutical sciences. “Our results suggest that chemical evolution could pave the way for the development of new therapies for a wide range of diseases.”
Gene silencing has been available for more than 20 years, and some FDA-approved drugs incorporate various versions of the technology, but none can distinguish a single point mutation in an RNA strand. The benefit of the Dz 46 enzyme is that it can identify and cut a specific genetic mutation, offering patients innovative and precision medical treatment.
The DNAzyme looks like the Greek letter omega and acts as a catalyst by speeding up chemical reactions. The left and right “arms” bind to the target region of the RNA. The loop binds to magnesium and folds and cuts the RNA at a very specific site. But generating DNA enzymes with robust multiple turnover activity under physiological conditions required some ingenuity, because DNA enzymes are normally highly dependent on magnesium concentrations not found inside a human cell.
“We solved that problem by reengineering the DNAzyme using chemistry to reduce its dependence on magnesium, and we did it in such a way that we could maintain high catalytic turnover activity,” Chaput said. “Ours is one of the first, if not the first, example of achieving that. The next steps are to advance Dz 46 to the point where it is ready for preclinical trials.”
Team members Kim Thien Nguyen, project scientist, and Turnee N. Malik, postdoctoral fellow, both from the Department of Pharmaceutical Sciences, also participated in this study.
The researchers and the UCI have filed provisional patent applications on the chemical composition and cleavage preference of Dz 46. Chaput is a consultant to the drug development company 1E Therapeutics, which supported this work.
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