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Basic RNA enzyme research promises single-molecule biosensors

ANN ARBOR, Mich.---Research aimed at teasing apart the workings of RNA enzymes eventually may lead to ways of monitoring fat metabolism and might even assist in the search for signs of life on Mars, according to University of Michigan researcher Nils Walter.

His latest work was published online in the Proceedings of the National Academy of Sciences June 24.

Walter and associates at U-M and colleague Xiaowei Zhuang and associates at Harvard University, use techniques that allow them to study single molecules of RNA enzymes, also known as ribozymes. Like the more familiar protein enzymes, RNA enzymes accelerate chemical reactions inside cells. Researchers want to learn how changes in ribozyme molecules affect their activity, both to better understand how evolution has shaped ribozymes to carry out their duties and to find ways of manipulating them for useful purposes.

In the recent research, Walter's group combined a technique called single-molecule fluorescence resonance energy transfer (FRET) with mathematical simulations to study a ribozyme involved in the replication of a tobacco-infecting virus. Just as a protein enzyme is not a static structure, a ribozyme also changes shape, cycling back and forth between its compact, catalytically active form and its inactive, extended form. Single-molecule FRET allowed the researchers to directly observe and measure how quickly the ribozyme switched forms and how these rates changed when various parts of the molecule were altered.

With the addition of mathematical simulations, the researchers also could investigate how changing parts of the ribozyme molecule affected its ability to catalyze chemical reactions. They were surprised to find that modifications they made anywhere on the molecule---even far from the site where the chemical reaction occurs---affected the rate of catalysis.

That's much like what is known to happen in protein enzymes, but until now there was no evidence that
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Contact: Nancy Ross Flanigan
rossflan@umich.edu
734-647-1853
University of Michigan
29-Jun-2004


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