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Science 20 March 1998:
Vol. 279. no. 5358, pp. 1940 - 1943
DOI: 10.1126/science.279.5358.1940
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Reports

RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting

Bianca Sclavi, Michael Sullivan, Mark R. Chance, * Michael Brenowitz, * Sarah A. Woodson *

Radiolysis of water with a synchrotron x-ray beam permits the hydroxyl radical-accessible surface of an RNA to be mapped with nucleotide resolution in 10 milliseconds. Application of this method to folding of the Tetrahymena ribozyme revealed that the most stable domain of the tertiary structure, P4-P6, formed cooperatively within 3 seconds. Exterior helices became protected from hydroxyl radicals in 10 seconds, whereas the catalytic center required minutes to be completely folded. The results show that rapid collapse to a partially disordered state is followed by a slow search for the active structure.

B. Sclavi, M. Sullivan, M. R. Chance, Department of Physiology and Biophysics, Center for Synchrotron Biosciences, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
M. Brenowitz, Department of Biochemistry, Center for Synchrotron Biosciences, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
S. A. Woodson, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA.
*   To whom correspondence should be addressed.

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