Monovalent cations use multiple mechanisms to resolve ribozyme misfolding

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Monovalent cations play crucial roles in RNA folding.
• The Tetrahymena ribozyme is a common model for studying these roles.
• The specific impact on the Candida ribozyme remains less understood.

Purpose of the Study:

• To investigate the effects of monovalent cations on Candida ribozyme folding.
• To determine how these ions influence the ribozyme's starting state and activity.
• To compare folding pathways influenced by different cation concentrations.

Main Methods:

• Studied the Candida ribozyme's folding kinetics.
• Assessed the impact of varying monovalent cation (Na+, Tris+) concentrations.
• Analyzed the formation of specific structural elements (J3/4:P6 triple, L2.1/L6 loops, P5abc).
• Compared folding pathways on the same energy landscape with Mg2+.

Main Results:

• Candida ribozyme requires 10x less monovalent cations for a new folding state.
• This state partially forms the J3/4:P6 base triple and resolves L2.1/L6 loop mispairing.
• Altered starting state with Mg2+ leads to faster core assembly and 5-10x increased activity.
• High monovalent cation concentrations resolve P5abc misfolding in prone states, moderately increasing activity.

Conclusions:

• Monovalent cations significantly alter the Candida ribozyme's folding initiation and efficiency.
• Optimized starting states driven by monovalent cations enhance ribozyme activity.
• Understanding these cation-specific effects is key for RNA structure-function studies.