Researchers from the Massachusetts Institute of Technology have taken a detailed look at how genes are turned into proteins in cells engineered with synthetic DNA sequences. When scientists design synthetic genes, they often focus on getting the right amount of messenger RNA (mRNA) made, assuming that more RNA will naturally lead to more protein. But this new research shows that things are not so simple.

Using a combination of tools that allow them to measure both RNA and protein levels in the same single cells, the team discovered that strong promoters (DNA sequences that kickstart gene activity) do more than just increase RNA production. They also boost how efficiently that RNA gets turned into protein. That means the same amount of RNA can lead to very different protein levels, depending on how the system is built.

To understand what was happening at the molecular level, the researchers used long-read direct RNA sequencing to map where transcription started and how RNA was processed. This allowed them to study the effects of different promoter and untranslated regions (UTRs) on gene expression. They also found that other elements, like the polyadenylation signal and the actual protein-coding region, could greatly influence the overall output of synthetic genes.

Altogether, this work provides a powerful framework for scientists building custom genes for use in research, biotechnology, and medicine. By looking closely at both transcription and translation, the team has laid the groundwork for designing more reliable genetic circuits in synthetic biology.