Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA

Area of Science:

• Structural Biology
• RNA Molecular Recognition
• Biochemistry

Background:

• Understanding RNA-ligand interactions is crucial for drug discovery and molecular biology.
• In vitro selection has generated RNA molecules with high specificity for small molecules.
• Theophylline is a key pharmaceutical compound, and its selective binding by RNA is of interest.

Purpose of the Study:

• To elucidate the three-dimensional structure of a high-affinity RNA-theophylline complex.
• To understand the molecular basis for the RNA's ability to discriminate theophylline from caffeine.
• To identify novel RNA structural motifs involved in ligand binding and specificity.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy was employed to determine the solution structure.
• High-affinity RNA selected in vitro was complexed with theophylline.
• Detailed structural analysis focused on hydrogen bonding and base-stacking interactions.

Main Results:

• A well-ordered binding pocket was identified, formed by interacting internal loops and base triples.
• The theophylline molecule is precisely positioned via hydrogen bonds and stacking interactions.
• Novel structural motifs, including base-zippers and a reversed sugar, were observed.
• Conserved core residues engage in multiple, overlapping tertiary interactions, stabilizing the complex.
• The RNA demonstrates high affinity and molecular discrimination, distinguishing theophylline from caffeine.

Conclusions:

• The determined RNA-theophylline complex structure reveals a sophisticated binding site assembled from interlocking motifs.
• This study highlights how complex tertiary interactions contribute to high affinity and ligand specificity in RNA.
• The findings provide a structural basis for RNA-based theophylline recognition and potential therapeutic applications.