Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated...

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Non-coding RNAs are key targets for novel therapeutics due to their regulatory roles.
• Phytochemicals (PCs) offer a rich source for drug development, with many possessing heterocyclic structures capable of interacting with nucleic acids.

Purpose of the Study:

• To investigate the interaction between phytochemicals and RNA.
• To elucidate RNA-mediated functions of phytochemicals using berberine (BRB) as a model.
• To identify specific RNA motifs that bind to phytochemicals.

Main Methods:

• Integrated approach combining RNA screening of a transcriptome library and sequence refinement.
• Nuclear Magnetic Resonance (NMR) spectroscopy for structure determination.
• Physicochemical analyses using berberine analogues.

Main Results:

• Identified a minimal RNA motif (cytosine bulge with U-A and G-U pairs) that selectively binds berberine.
• Demonstrated the importance of electrostatic and stacking interactions in sequence-selective binding and RNA stabilization.
• Highlighted the role of planar heterocyclic structures in phytochemical-RNA interactions.

Conclusions:

• Phytochemicals can selectively target specific functional RNAs through interactions with minimal RNA motifs.
• This interaction mechanism provides a basis for developing novel RNA-targeting therapeutics derived from phytochemicals.
• The study provides a framework for systematic investigation of phytochemical-RNA interactions for future drug development.