Cooperative tertiary interaction network guides RNA folding

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Noncoding RNAs fold into complex 3D structures essential for their regulatory functions.
• Understanding the folding mechanisms of RNAs, particularly the role of tertiary interactions, is crucial.

Purpose of the Study:

• To investigate how noncoding RNAs achieve unique 3D structures with limited tertiary interaction motifs.
• To elucidate the role of cooperativity in RNA folding and the formation of native states.

Main Methods:

• Site-directed mutagenesis of tertiary interactions in a group I ribozyme.
• Small-angle X-ray scattering (SAXS) to probe structural perturbations.
• Enzyme activity assays, hydroxyl radical footprinting, and native polyacrylamide gel electrophoresis (PAGE) to assess folding and stability.

Main Results:

• Most tertiary interactions had minimal impact on the native state's stability.
• Cooperative linkage between core and peripheral structural motifs was observed in folding intermediates.
• This cooperativity was dependent on native helix orientation and suppressed nonnative structures.

Conclusions:

• RNA folding is guided by an emergent cooperative interaction network, not solely by individual tertiary interactions.
• Cooperativity likely evolved to ensure the formation of a unique and stable native fold in noncoding RNAs.