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Revealing Secrets of RNA

August 2, 2011

(Ivanhoe Newswire) — The ability to tag proteins with a green fluorescent light to watch how they behave inside cells so revolutionized the understanding of protein biology that it earned the scientific teams who developed the technique Nobel Prizes in 2008. Now, researchers at Weill Cornell Medical College have developed a similar fluorescent tool that can track the mysterious workings of the various forms of cellular RNA.

“These fluorescent RNAs offer us a tool that will be critical for understanding the diverse roles that RNA plays in human biology,” the study’s senior author, Dr. Samie Jaffrey, an associate professor of pharmacology at Weill Cornell Medical College, was quoted as saying.

The list of known types of RNA has grown rapidly over the past several years “” from messenger RNA that codes for proteins, to diverse “non-coding” RNAs that affect translation and gene expression, and in some cases bind to proteins and regulate their function “” yet little is known about how these RNAs work, the researchers say.
The study’s first author, Dr. Jeremy Paige, who conducted the research as a graduate student in pharmacology at Weill Cornell Medical College, adds that the new technology may provide insights into the development of common disorders. “More and more diseases are being linked to misregulation of RNA, but without being able to see the RNA, we can’t understand how these processes lead to disease.”We hope our RNA mimics of GFP open up the road to discovery,” Dr. Paige said.

To make an RNA that functions like GFP, the Weill Cornell investigators took advantage of the ability of RNA to fold into complex three-dimensional shapes. Their goal was to create two new entities: a synthetic RNA sequence that would adopt a specific shape, and a small molecule that would bind to the new RNA and begin to fluoresce. “These were two huge challenges,” says Dr. Jaffrey. “One challenge was to come up with an RNA sequence that could ‘switch on’ a small molecule. The other big hurdle was to find a small molecule that would fluoresce only when we wanted it to and would not be toxic to cells.”

They tried a number of molecules, most of which stuck to oily lipids in the cell membrane and started fluorescing, or they would kill the cell. Finally, the team realized that GFP itself had a molecule, a fluorophore, within it that switched its light on when it was bound in a certain way within the protein. They created chemical molecules based on the shape of this fluorophore and then developed an artificial RNA sequence, or “aptamer,” that held the fluorophore in exactly the same way that GFP held its fluorophore. They named this RNA “Spinach” for its bright green fluorescence.

The researchers went even further. They also developed several other RNA-fluorophore pairs, in addition to Spinach, that each emits a different fluorescent color, just as GFP has been evolved to exhibit a palette of colors that helps researchers track many proteins at once.

“There is still a lot of mystery surrounding RNA in biology. Fluorescent labeling and imaging has proved to be a powerful tool for scientists in the past, and we are hoping that Spinach too will be a tool that helps accelerate scientific discovery,” said Dr. Paige.

SOURCE: Science, published online August 2, 2011




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