Using triple-helix-forming Peptide nucleic acids for sequence-selective recognition of double-stranded RNA

Area of Science:

• Biochemistry
• Molecular Biology
• Chemical Biology

Background:

• Non-coding RNAs regulate gene expression and form complex double-helical structures.
• Targeting these structures is crucial for biological studies and medical applications.
• Existing methods for specific RNA recognition are limited.

Purpose of the Study:

• To develop a novel strategy for sequence-selective recognition and inhibition of double-stranded RNA (dsRNA).
• To utilize triple-helix-forming peptide nucleic acids (PNAs) for targeting dsRNA.
• To enable precise control over gene expression and explore therapeutic interventions.

Main Methods:

• Design and synthesis of chemically modified PNA monomers, including 2-aminopyridine (M), 2-pyrimidinone (P), and 3-oxo-2,3-dihydropyridazine (E).
• Solid-phase synthesis of PNA oligomers.
• High-performance liquid chromatography (HPLC) for PNA purification.
• Isothermal titration calorimetry (ITC) to measure dsRNA binding affinity.

Main Results:

• Demonstrated sequence-selective binding of modified PNAs to dsRNA in the major groove.
• Achieved strong triple-helical binding under physiologically relevant conditions.
• Successfully recognized isolated pyrimidines in the purine-rich strand of the RNA duplex.
• Detailed protocols for PNA synthesis and characterization were established.

Conclusions:

• This PNA-based strategy offers a powerful tool for sequence-selective dsRNA recognition and inhibition.
• The developed methodology facilitates fundamental biological research and opens avenues for novel medical treatments.
• Chemically modified PNAs provide a versatile platform for targeting specific RNA structures.