Steffen Klein spent six months in a lab in Seattle, away from his usual microscopy work at EMBL Heidelberg in Germany. The goal of his detour halfway around the world was to learn how to design proteins from scratch using artificial intelligence—proteins that had never existed in nature. When he returned home, he helped create something that could change how scientists see inside living cells.

The tool is called NovoTags, a new class of synthetic fluorescent protein tags developed through a collaboration between the Baker Lab at the Institute for Protein Design in Seattle, the Lavis Lab at Janelia Research Campus in Virginia, and the Mahamid Group at EMBL Heidelberg in Germany. Their findings were published in the journal Science.

Klein, a structural biologist in EMBL's Mahamid Group, worked alongside Long Tran, a graduate student in the Baker Lab. Tran first designed NovoTags to bind to three Janelia Fluor dyes that span the visible color spectrum. These small, AI-designed proteins can be attached to other proteins scientists want to study. When the dyes bind to the tags, they light up, making previously invisible molecules visible under powerful microscopes.

Klein then took the work further, developing a version called NovoSplit—a molecular switch that only activates when its target dye is added to the cell. This gives researchers precise control over when and where tagging occurs.

Back at EMBL, Klein tested the NovoTags in living human cells using advanced microscopy techniques, including a method called live STED microscopy and fluorescence lifetime imaging microscopy (FLIM). By combining color information with how long molecules glow, the team showed it may be possible to track up to 30 different proteins at the same time—a major leap from current methods.

David Baker, who led the Baker Lab, received the Nobel Prize in Chemistry in 2024 for pioneering AI-driven protein design. The Baker and Lavis labs are now expanding the NovoTag collection with support from AI@HHMI, a $500 million initiative by the Howard Hughes Medical Institute. Luke Lavis, senior group leader at Janelia, said de novo designed proteins combined with synthetic dyes could soon become the go-to tools for labeling molecules in living systems.

The NovoTag sequences and complementary dyes are freely available to any scientist who wants to use them.