Sequence-specific recognition of structured RNA by triplex-forming peptide nucleic acids

• Published in: Methods in enzymology Vol. 623; p. 401
• Main Authors: Hnedzko, Dziyana, Rozners, Eriks
• Format: Journal Article
• Language: English
• Published: United States 2019
• Subjects: Base Sequence; Binding Sites; Chromatography, High Pressure Liquid - methods; Colorimetry - methods; Drug Design; Nucleic Acid Conformation - drug effects; Peptide Nucleic Acids - chemistry; Peptide Nucleic Acids - pharmacology; RNA, Double-Stranded - chemistry; RNA, Double-Stranded - metabolism; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods; Spectrophotometry, Ultraviolet - methods; Sequence selective RNA recognition; PNA; Modified nucleobases; Triple helix; ITC; Peptide nucleic acid; Isothermal titration calorimetry
• ISSN: 1557-7988
• DOI: 10.1016/bs.mie.2019.04.003

While <2% of DNA encodes for functional proteins, >70% is transcribed into RNA. Although the function of most RNA transcripts is unknown, such non-coding RNAs are attractive targets for molecular recognition because of the potentially important roles they play in regulation of gene expression and development of disease. In this chapter, we describe peptide nucleic acids (PNAs) that form sequence-specific triple helices with double-stranded RNA (dsRNA). We provide protocols for sequence design and biophysical characterization of PNAs and discuss first examples where such PNAs have been used for functional modulation of dsRNA. The triplex-forming PNAs represent a new approach for RNA recognition that may find future applications in fundamental science, biotechnology and medicine.