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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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Increased ribozyme activity in crowded solutions.

Ravi Desai1, Duncan Kilburn, Hui-Ting Lee

  • 1From the T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore, Maryland 21218.

The Journal of Biological Chemistry
|December 17, 2013
PubMed
Summary
This summary is machine-generated.

Molecular crowding stabilizes the Azoarcus group I ribozyme, enhancing its biochemical activity. Specific crowders like PEG and Ficoll increase RNA cleavage by favoring the active ribozyme structure.

Keywords:
Macromolecular CrowdingPEGRNA CatalysisRNA FoldingRibozymeX-ray Scattering

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Noncoding RNAs function within the crowded cellular environment.
  • Molecular crowders were previously shown to stabilize the Azoarcus group I ribozyme structure.
  • Stabilization by crowders allows ribozyme folding at low magnesium concentrations.

Purpose of the Study:

  • To investigate the effect of molecular crowding on the biochemical activity of the Azoarcus group I ribozyme.
  • To determine if different types of crowders influence ribozyme activity differently.
  • To understand how crowding affects the Mg(2+) dependence of ribozyme function.

Main Methods:

  • RNA cleavage assays were employed to measure ribozyme activity.
  • Experiments were conducted using PEG, Ficoll, and sucrose as molecular crowders.
  • The Mg(2+) concentration dependence of ribozyme activity was analyzed under crowded and dilute conditions.

Main Results:

  • PEG and Ficoll crowders significantly increased the biochemical activity of the ribozyme.
  • Sucrose did not enhance ribozyme activity.
  • Molecular crowding lowered the Mg(2+) threshold for detectable activity and increased overall RNA cleavage.
  • Reaction rates correlated with the fraction of active ribozyme after viscosity correction.

Conclusions:

  • Molecular crowders stabilize the native structure of the Azoarcus group I ribozyme.
  • Crowding favors the biologically active ribozyme conformation over inactive folding intermediates.
  • This stabilization enhances the catalytic efficiency of the ribozyme.