Until about 20 years ago, scientists relied on chemical fluorescent dyes to make biological molecules visible. To look inside cells, stain organelles, and perform other imaging experiments, chemistry was the method used. Chemistry was subsequently replaced by GFP, a glowing green jellyfish protein.

Novel rhodamine dyes that were synthesized using the new method. (Jonathan B. Grimm)

Scientists used a genetic trick to tack GFP onto other cellular proteins; similar to forcing the proteins to hold a glow stick. That trick gave researchers a simpler way to trace proteins’ movements under a microscope without using expensive synthetic dyes. GFP, however, is a relatively “clunky” molecule built out of the limited set of natural amino acids; it is not always bright enough to reveal what scientists are trying to see.

Scientists recently developed a method for fine-tuning the structure of rhodamine dyes — which are extremely bright and cell-permeable — and created a colorful palette of fluorescent molecules. Rhodamines have a basic four-ringed design with groups of atoms protruding from different parts of the rings. In previous work, the scientists developed strategies for coarse-tuning dyes. By cutting out an entire appendage, it was possible to make a green dye; by popping in a silicon atom, it was possible to create a red dye. Carefully placing just a few new atoms in the dye structure enabled the color and chemical properties of the dyes to be fine-tuned, allowing many shades of green from a single scaffold.

Swapping out specific chemical building blocks in rhodamines can generate nearly any color. This offers scientists a way to adjust the properties of existing dyes deliberately, making them bolder, brighter, and more cell-permeable. Such an expanded palette of dyes could help researchers better illuminate the inner workings of cells, and could allow chemists to synthesize hundreds of different colors.

A variety of strategies can be used to get the bright dye molecules onto the protein to be studied. Then, researchers can zero in on the lit-up protein and watch it move and interact with other molecules without the usual background fuzziness. The dyes are bright enough to capture molecules in action in just a millisecond.

The dyes are synthesized in a single step with inexpensive ingredients, making the dyes less expensive than commercial alternatives at just cents per vial. The low cost has allowed the team to share their work with scientists around the world; they have shipped thousands of vials to hundreds of different labs.

For more information, contact Meghan Rosen at This email address is being protected from spambots. You need JavaScript enabled to view it.; 301-215-8859.

Tech Briefs Magazine

This article first appeared in the August, 2019 issue of Tech Briefs Magazine.

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