Design of Fluorescent Peptide Nucleic Acid Probes Carrying Cyanine Dyes for Targeting Double-Stranded RNAs for Analytical Applications

Abstract

With the increasing knowledge about the diverse roles of RNAs within cells, much attention has been paid to the development of RNA-binding fluorescent probes for the study of RNA functions. Especially, the probes for double-stranded RNA (dsRNA) structures are highly useful given the importance of the secondary and tertiary RNA structures on their biological functions. This account describes our recent efforts to develop synthetic fluorescent probes based on peptide nucleic acids (PNAs) carrying fluorogenic cyanine dyes for targeting the overhang structures of dsRNAs with a view toward the analysis of the intracellular delivery process of small interfering RNAs. We also describe the design of triplexforming PNA probes carrying cyanine dye base surrogates for the sequence-selective detection of dsRNAs.