Hinge stiffness is a barrier to RNA folding

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Cation-mediated RNA folding involves a balance of forces to achieve biologically active conformations.
• The Tetrahymena thermophila ribozyme folds via rapid collapse followed by tertiary contact formation, influenced by Mg2+.

Purpose of the Study:

• To investigate the role of chain flexibility in the rapid collapse phase of RNA folding.
• To probe the Mg2+-dependent folding dynamics of the P4-P6 domain of the Tetrahymena ribozyme.

Main Methods:

• Studied the time evolution of P4-P6 domain folding using global and local measures.
• Analyzed folding as a function of varying Mg2+ concentrations.

Main Results:

• Mg2+ significantly accelerates RNA collapse but does not accelerate tertiary contact formation.
• At 10 mM Mg2+, a stiff hinge limits P4-P6 folding rate; higher concentrations shift the rate-limiting step.
• Diverging rates of compaction and tertiary contact formation observed with increasing Mg2+ concentration.

Conclusions:

• Chain stiffness is a critical factor in RNA folding dynamics.
• Mg2+ concentration differentially affects the rates of RNA collapse and tertiary structure formation.
• The rate-limiting step in P4-P6 domain folding transitions from hinge bending to tertiary contact formation with increasing Mg2+.