Slow conformational dynamics at C2'-endo nucleotides in RNA

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• RNA molecules exhibit local conformational dynamics across a wide range of timescales, from picoseconds to minutes.
• Slower motions are critical for RNA folding, ligand binding, and ribonucleoprotein assembly but are challenging to study in large, complex RNAs.
• RNA Selective 2′-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) chemistry probes nucleotide flexibility by monitoring acylation at the ribose 2'-hydroxyl position.

Purpose of the Study:

• To investigate the role of local RNA conformational dynamics, particularly C2'-endo conformations, in governing RNA reactivity and function.
• To characterize the timescales of conformational changes in RNA using modified SHAPE chemistry.
• To identify potential molecular switches within RNA structures that influence biological processes.

Main Methods:

• Utilized RNA SHAPE chemistry with varying electrophilicity of acylating reagents to probe RNA conformational dynamics.
• Monitored nucleotide flexibility and reactivity across distinct time domains.
• Applied methods to both model RNA systems and a large RNA with a defined tertiary structure.

Main Results:

• Demonstrated that C2'-endo nucleotides are not uniformly reactive to SHAPE reagents; reactivity depends on the reagent's electrophilicity and the nucleotide's conformational state.
• Identified specific C2'-endo nucleotides exhibiting exceptionally slow conformational changes (on the order of 10^-4 s^-1).
• Showed that these slow dynamics are observable in both model and complex biological RNA structures.

Conclusions:

• The C2'-endo conformation alone does not dictate SHAPE reactivity; rather, the dynamics of conformational interconversion are key.
• Certain C2'-endo nucleotides function as slow molecular switches due to their unique local dynamics.
• These slow dynamics likely play significant, yet underappreciated, roles in RNA folding pathways and functional mechanisms.