RNAs are key biomolecules that regulate all protein production in the body. The proteins then go on to control how cells function. To artificially control this production, synthetic biologists have manufactured RNA tools. A new study seen in Nucleic Acids Research by the Hirohide Saito laboratory explores how a simple substitution of uridine, one of four bases found in RNA molecules, with N¹-methylpseudouridine (1mΨ), a naturally existing base, enhances the performance of RNA tools.

Modifying the nucleic acid bases of RNA molecules with naturally existing structural variations of the bases is a common approach used by synthetic biologists. Although these modified bases are natural, they can elicit an immune response in the cell.

"Our challenge is to identify which modification(s) maximize performance while preserving safety. In this study we looked at many types of modifications and their performance in human cells," explains Dr. Yi Kuang, who had worked on the project in the Saito lab but has since moved to the Hong Kong University of Science and Technology as an assistant professor.

Most synthetic biology tools are made of DNA. Both DNA and RNA molecules are constituted of four bases, but DNA tools are easier to produce. At the same time, DNA is only found in the nucleus of the cell. Should the DNA tools incorporate there, they risk permanent mutational effects. RNA tools do not have this risk. Moreover, they quickly degrade in the cell.

The Saito lab has therefore focused its attention on RNA tools, including their RNA switch, which is designed to sense the expression of microRNA or protein in cells. In the current study, the researchers tested several base modifications and their combinations on the performance of the RNA.

"We tested the 1mΨ modification in several human cells using different RNA switches and found each time little-to-no immune response and better sensing performance," says Kuang.

Exploring the reason, the researchers found that 1mΨ can bypass cell the innate immune response and may also strengthen binding between the RNA switch and its target molecules.

Saito states that one of the major appeals of 1mΨ "is that this base modification is commercially available and is easy to be incorporated into RNA tools. There is still much to learn about 1mΨ, but 1mΨ expands the applicability and drives forward RNA switch to tackle real-world issues like cell therapies."

• doi: 10.1093/nar/gkaa070