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Science 24 May 2002:
Vol. 296. no. 5572, pp. 1473 - 1476
DOI: 10.1126/science.1069013
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Reports

Correlating Structural Dynamics and Function in Single Ribozyme Molecules

Xiaowei Zhuang,1* Harold Kim,1 Miguel J. B. Pereira,2 Hazen P. Babcock,1* Nils G. Walter,2dagger Steven Chu1dagger

We have studied the correlation between structural dynamics and function of the hairpin ribozyme. The enzyme-substrate complex exists in either docked (active) or undocked (inactive) conformations. Using single-molecule fluorescence methods, we found complex structural dynamics with four docked states of distinct stabilities and a strong memory effect where each molecule rarely switches between different docked states. We also found substrate cleavage to be rate-limited by a combination of conformational transitions and reversible chemistry equilibrium. The complex structural dynamics quantitatively explain the heterogeneous cleavage kinetics common to many catalytic RNAs. The intimate coupling of structural dynamics and function is likely a general phenomenon for RNA.

1 Department of Physics, Stanford University, Stanford, CA 94305, USA.
2 Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
*   Present address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

dagger    To whom correspondence should be addressed. E-mail: nwalter{at}umich.edu, schu{at}stanford.edu

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