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Related Experiment Videos

Cation-specific structural accommodation within a catalytic RNA.

Dominic Lambert1, Joyce E Heckman, John M Burke

  • 1Department of Microbiology and Molecular Genetics, University of Vermont, 220B Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405, USA.

Biochemistry
|January 18, 2006
PubMed
Summary

Cobalt(III) hexaammine supports hairpin ribozyme folding and activity, mediating unique photocrosslinks. These findings suggest a distinct catalytic core structure compared to magnesium-bound ribozymes.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Metal ions are crucial for the folding and catalytic activity of ribozymes.
  • The hairpin ribozyme's catalytic mechanism and structure are influenced by the specific metal ions involved in its folding.
  • Cobalt(III) hexaammine ([Co(NH3)6]3+) is investigated as a metal ion that supports ribozyme folding and activity.

Purpose of the Study:

  • To investigate the role of cobalt(III) hexaammine in hairpin ribozyme folding and catalysis.
  • To identify specific internucleotide photocrosslinks mediated by [Co(NH3)6]3+ and their impact on ribozyme structure and activity.
  • To propose a model for the [Co(NH3)6]3+-mediated catalytic core.

Main Methods:

  • Site-directed photocrosslinking using cobalt(III) hexaammine.

Related Experiment Videos

  • Cleavage kinetics assays with modified ribozyme variants.
  • Structural modeling using MC-SYM software.

    • Main Results:

    • Cobalt(III) hexaammine mediates specific internucleotide photocrosslinks, some retaining catalytic ability.
    • These crosslinks indicate a different active core structure compared to Mg2+-bound ribozymes.
    • Substrate residues U+2 and C+3 adopt distinct conformations in the presence of [Co(NH3)6]3+, affecting cleavage rates.

    Conclusions:

    • The active core structure of the hairpin ribozyme is influenced by the coordinating metal ion.
    • [Co(NH3)6]3+ organizes a distinct catalytic core, differing from Mg2+-mediated structures.
    • A model for the [Co(NH3)6]3+-mediated catalytic core is proposed, consistent with experimental data.