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Compaction of a Bacterial Group I Ribozyme Coincides with the Assembly of Core Helices

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Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562, T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218-2685, and Department of Materials Science and Engineering and Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20472
Cite this: Biochemistry 2004, 43, 6, 1746–1753
Publication Date (Web):January 17, 2004
Copyright © 2004 American Chemical Society

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    Counterions are critical to the self-assembly of RNA tertiary structure because they neutralize the large electrostatic forces which oppose the folding process. Changes in the size and shape of the Azoarcus group I ribozyme as a function of Mg2+ and Na+ concentration were followed by small angle neutron scattering. In low salt buffer, the RNA was expanded, with an average radius of gyration (Rg) of 53 ± 1 Å. A highly cooperative transition to a compact form (Rg = 31.5 ± 0.5 Å) was observed between 1.6 and 1.7 mM MgCl2. The collapse transition, which is unusually sharp in Mg2+, has the characteristics of a first-order phase transition. Partial digestion with ribonuclease T1 under identical conditions showed that this transition correlated with the assembly of double helices in the ribozyme core. Fivefold higher Mg2+ concentrations were required for self-splicing, indicating that compaction occurs before native tertiary interactions are fully stabilized. No further decrease in Rg was observed between 1.7 and 20 mM MgCl2, indicating that the intermediates have the same dimensions as the native ribozyme, within the uncertainty of the data (±1 Å). A more gradual transition to a final Rg of approximately 33.5 Å was observed between 0.45 and 2 M NaCl. This confirms the expectation that monovalent ions not only are less efficient in charge neutralization but also contract the RNA less efficiently than multivalent ions.

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     Supported by the National Research Council Postdoctoral Associateship Program (U.A.P.-S.), the National Institute of Standards and Technology, and the National Institutes of Health (S.A.W.). The Center for High-Resolution Neutron Scattering at the NIST is sponsored by the NSF (DMR-9986442).


     Corresponding authors:  U.A.P.-S. (tel, 301-975-8395; fax, 301-921-9847; e-mail, [email protected]), R.M.B. (tel, 301-405-7313; fax, 301-314-9601; e-mail, [email protected]), and S.A.W. (tel, 410-516-2015; fax, 410-516-4118; e-mail, [email protected]).


     The first two authors contributed equally to this work.

     Center for Neutron Research, NIST.


     T. C. Jenkins Department of Biophysics, Johns Hopkins University.

     Department of Materials Science and Engineering, University of Maryland.

     Institute for Physical Sciences and Technology, University of Maryland.

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    Two figures showing ribonuclease T1 digestion of ribozyme RNA and self-splicing assays and one table listing the Mg2+ dependence of RNase T1 digestion of 10 mg/mL ribozyme. This material is available free of charge via the Internet at

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