Green fluorescent protein extracted from luminescent jellyfish has been used as a marker for gene expression and protein localization in a number of biological systems. Despite the widespread use of this fluorescing dye, little is known about how its structural features promote fluorescence. For years, the search for new fluorescing proteins was limited to species that exhibit bioluminescence. Now a group of biologists at the Russian Academy of Science's Institute of Ecology and Evolution and Institute of Bioorganic Chemistry has expanded the scope of the search. The team surmised that biochemical modules are behind the assembly of bioluminescence systems. That is, various components of bioluminescent systems are found in organisms that do not exhibit bioluminescence, so the sought-after fluorescent proteins might not be the only source for biological markers. Coral reefs -- with their wide variety of naturally fluorescent colors -- were a natural candidate for consideration. "Coral reefs contain any type of protein a scientist may wish for a particular project," said Mikhail V. Matz, a biologist involved in the research. "Before, there was no choice, since there was only one protein." Pure gene sequences To test whether coral reefs would yield fluorescing molecules, Matz and his colleagues took microscopic samples of corals from a private aquarium. Using a technique they called the "PCR-suppression effect," they were able to rid the samples of undesirable DNA fragments and obtain pure target sequences. The researchers scored hits in all five coral species they studied, according to a paper they published in the October 1999 issue of Nature Biotechnology. Like green fluorescent protein, the new materials can synthesize fluorophores from within their own structure and without aid from exterior components other than molecular oxygen. Commercial applications related to the group's work are in the offing. "The red fluorescent protein already initiated a new line of products from Clontech Laboratories Inc.," Matz said. "People are already using the protein in their research. I think in several months first reports will appear." As for future research, the group will study the mechanisms of fluorophore formation in the red dyes and work toward adapting new proteins for various biotechnological applications.