A hammerhead ribozyme selects mechanically stable conformations for catalysis against viral RNA

Area of Science:

• Molecular Biology
• Biochemistry
• Biophysics

Background:

• Ribozymes are RNA enzymes with diverse biological roles and therapeutic potential.
• Hammerhead ribozymes are small, well-characterized RNA enzymes, but their catalytic mechanisms remain incompletely understood.
• The role of conformational dynamics in ribozyme catalysis is a key area of investigation.

Purpose of the Study:

• To elucidate the catalytic mechanism of a mini hammerhead ribozyme.
• To investigate the role of conformational dynamics in hammerhead ribozyme activity.
• To explore the interaction of magnesium ions with ribozyme conformers.

Main Methods:

• Single-molecule magnetic tweezers to probe mechanical conformational selection.
• Molecular dynamics simulations to support experimental findings.
• Utilized a mini hammerhead ribozyme targeting a SARS-CoV-2 RNA sequence.

Main Results:

• Identified a set of five distinct mechanical conformers for the mini hammerhead ribozyme.
• Demonstrated that magnesium ions selectively activate a specific conformer for catalysis.
• Revealed a concerted catalysis mechanism involving mechanical conformational selection.

Conclusions:

• The study clarifies the hammerhead ribozyme's catalytic mechanism through conformational dynamics.
• Magnesium ion-mediated selection of active conformers is crucial for ribozyme function.
• Findings have implications for developing ribozymes as biotechnological tools and antiviral therapeutics.