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

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Abstract
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.