[Formation of spatial structure of RNA molecules]

Area of Science:

• Molecular Biology
• Biophysics
• Computational Biology

Context:

• RNA molecules, such as transfer RNA (tRNA) and ribozymes, fold into complex three-dimensional structures essential for their function.
• Understanding the folding pathways and critical nucleotides is crucial for deciphering RNA's biological roles.

Purpose:

• To review experimental and theoretical methods for investigating RNA folding.
• To identify key nucleotides involved in the folding of tRNA and ribozymes.
• To evaluate the accuracy of current RNA folding models.

Summary:

• This review examines experimental (e.g., SHAPE method) and theoretical approaches to RNA folding.
• It highlights that nucleotides in the D- and T-loop regions of tRNA are not part of the core folding nucleus.
• The widely accepted hierarchical folding model is challenged for tRNA folding based on new evidence.

Impact:

• Challenges the long-standing hierarchical folding model for tRNA.
• Provides insights into the non-critical role of D- and T-loop nucleotides in initial tRNA folding.
• Discusses algorithms and software for predicting RNA secondary structures and modeling folding processes.