Cellular Small Molecules Contribute to Twister Ribozyme Catalysis.

Area of Science:

• Biochemistry
• Molecular Biology
• RNA Catalysis

Background:

• Self-cleaving ribozymes are RNA molecules with catalytic activity.
• Four catalytic strategies (α, β, γ, δ) describe ribozyme mechanisms.
• The twister ribozyme's rapid self-cleavage is currently explained by these four strategies.

Purpose of the Study:

• To investigate the role of small molecules in ribozyme catalysis.
• To determine if cellular small molecules can enhance ribozyme activity.
• To elucidate the mechanism by which small molecules affect ribozyme function.

Main Methods:

• Assessing the catalytic rate of the wild-type twister ribozyme.
• Testing the effect of various buffers and biological small molecules (imidazole, amino acids, amino sugars) on ribozyme activity at biological pH.
• Utilizing Brønsted plots to analyze the mechanism of small molecule involvement.

Main Results:

• Moderate concentrations of buffers and diverse biological small molecules enhanced twister ribozyme self-cleavage rates up to 5-fold.
• This enhancement is comparable to effects seen with protein enzymes.
• Brønsted plots indicate small molecules facilitate proton transfer, likely through δ (leaving group stabilization) catalysis.

Conclusions:

• Cellular small molecules can significantly enhance ribozyme catalytic rates.
• These molecules may overcome limitations in RNA's functional diversity.
• Small molecules have the potential to play a crucial role in the in vivo catalytic mechanisms of many ribozymes.