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Science 21 March 2003:
Vol. 299. no. 5614, pp. 1892 - 1895
DOI: 10.1126/science.1081338
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Reports

Identifying Kinetic Barriers to Mechanical Unfolding of the T. thermophila Ribozyme

Bibiana Onoa,1*dagger Sophie Dumont,2* Jan Liphardt,34 Steven B. Smith,1 Ignacio Tinoco Jr.,34 Carlos Bustamante1234ddagger

Mechanical unfolding trajectories for single molecules of the Tetrahymena thermophila ribozyme display eight intermediates corresponding to discrete kinetic barriers that oppose mechanical unfolding with lifetimes of seconds and rupture forces between 10 and 30 piconewtons. Barriers are magnesium dependent and correspond to known intra- and interdomain interactions. Several barrier structures are "brittle," breakage requiring high forces but small (1 to 3 nanometers) deformations. Barrier crossing is stochastic, leading to variable unfolding paths. The response of complex RNA structures to locally applied mechanical forces may be analogous to the responses of RNA during translation, messenger RNA export from the nucleus, and viral replication.

1 Department of Physics and Department of Molecular and Cell Biology and Howard Hughes Medical Institute,
2 Biophysics Graduate Group,
3 Department of Chemistry, University of California, Berkeley, CA 94720, USA.
4 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
*   These authors contributed equally to this work.

dagger    Present address: DuPont Company Experimental Station, Post Office Box 80328, Wilmington, DE 19880-0328, USA.

ddagger    To whom correspondence should be addressed. E-mail: carlos{at}alice.berkeley.edu

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