Design of triplex-forming peptide nucleic acid-based fluorescent probes for forced intercalation sensing of double-stranded RNA structures

The diverse functional roles of RNA within cells have led to a growing interest in developing RNA-binding fluorescent probes to investigate RNA functions. In particular, the probes for double-stranded RNA (dsRNA) structures are of significant value given the importance of the secondary and tertiary RNA structures on their biologic functions. This review highlights our recent efforts on the development of triplex-forming peptide nucleic acid (TFP)-based probes for fluorescence sensing of dsRNA structures. We demonstrated that the forced intercalation of asymmetric cyanine dyes integrated as base surrogate within the probes was useful for achieving significant light-up response toward target dsRNAs. We also showed that the TFP probes conjugated with small RNA-binding molecules facilitated the fluorescence sensing of biologic relevant dsRNAs containing unpaired nucleobases. The binding and fluorescence signaling functions of such probes were discussed, emphasizing their potential as analytical tools for studying dsRNA structures.