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Conversation 11: No. 2

category image Volume: Conversation 11
Issue Number 2
May 2000
ISBN 0-940030-81-0

The Early Folding Intermediates of the TetrahymenaRibozyme are Kinetically Trapped

The ?RNA folding problem? is a fundamental and challenging question in contemporary biophysics. Understanding the mechanism(s) by which RNA molecules fold into compact structures capable of biological activity is important because RNA folding is closely tied to cellular regulation and metabolism and catalytic RNAs are potential reagents for gene therapy. Unlike the ?protein folding problem? which has been under study for many decades, the study of RNA tertiary structure stability and folding is a relatively new field of endeavor. Thus, a detailed understanding of both the thermodynamics and kinetics of RNA folding are only now beginning to emerge.

Kinetic traps have been observed in the late folding steps of the Tetrahymenaribozyme. In this study we extend our ?synchrotron footprinting? analysis of the Tetrahymenaribozyme (Sclavi, et al., Science 279, 1940-1943, 1998) to probe the potential presence of kinetic traps in other steps in the folding mechanism. Examination of the folding in 3M urea demonstrates a significant increase in the rates of folding for early folding steps in the formation of the ribozyme tertiary structure. These data support the conclusion of Williamson and co-workers that the rate-limiting step in the folding of the Tetrahymena ribozyme is kinetically trapped by native interactions (Rook et al., J. Mol. Bio., 281, 609-620, 1998). Kinetic trapping also occurs in the formation of intermediates earlier in the folding reaction, and in these cases non-native interactions may also play a role in the barrier to folding.

Corie Y. Ralston1
Bianca Sclavi1a
Michael Brenowitz1
Michael Sullivan1
and Mark R. Chance1,2

Center for Synchrotron Biosciences
1Department of Physiology and Biophysics
2Department of Biochemistry
Albert Einstein College of Medicine of Yeshiva University
1300 Morris Park Avenue
Bronx, New York 10461
and National Synchrotron Light Source
Brookhaven National Labs
Upton, NY 11973
aCurrent Address:
Unite de Physiocochimie des Macromolecules Biologiques
Institut Pasteur
25 Rue du Roux
75015 Paris, France

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