Compaction of a Bacterial Group I Ribozyme Coincides with the Assembly of Core Helices
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 Mg{sup 2+} and Na{sup +} concentration were followed by small angle neutron scattering. In low salt buffer, the RNA was expanded, with an average radius of gyration (R{sub g}) of 53 {+-} 1 Angstroms. A highly cooperative transition to a compact form (R{sub g} = 31.5 {+-} 0.5 Angstroms) was observed between 1.6 and 1.7 mM MgCl{sub 2}. The collapse transition, which is unusually sharp in Mg{sup 2+}, 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 Mg{sup 2+} 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 MgCl{sub 2}, indicating that the intermediates have the same dimensions as the native ribozyme, within the uncertainty of the data ({+-} 1 Angstroms). A more gradual transition to a final R{sub g} of approximately 33.5 Angstroms 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.
- Research Organization:
- Brookhaven National Laboratory (BNL) National Synchrotron Light Source
- Sponsoring Organization:
- Doe - Office Of Science
- DOE Contract Number:
- AC02-98CH10886
- OSTI ID:
- 913646
- Report Number(s):
- BNL--78214-2007-JA
- Journal Information:
- Biochemistry, Journal Name: Biochemistry Vol. 43; ISSN 0006-2960; ISSN BICHAW
- Country of Publication:
- United States
- Language:
- English
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