Sequence-Selective Recognition of Double-Stranded RNA

Abstract

The important role that noncoding RNA plays in cell biology makes it an attractive target for molecular recognition. However, the discovery of small molecules that bind such double-stranded RNA (dsRNA) selectively and may serve as biochemical probes and potential drug leads has been relatively slow. The surface of dsRNA is relatively uniform, dominated by negatively charged phosphates, and presents little opportunity for the traditional shape-selective molecular recognition. On the other hand, hydrogen-bonded base pairing is the key feature of nucleic acids and, therefore, inherently the most effective way of sequence-selective recognition of RNA. This chapter reviews recent progress in developing oligonucleotide analogues for selective binding to dsRNA. The emphasis is on hydrogen bonding to nucleobases, such as triple helix formation between RNA and peptide nucleic acids (PNAs). PNA having cationic nucleobase modifications binds to dsRNA with low nanomolar affinity and excellent sequence selectivity under physiologically relevant conditions. PNA is uniquely selective ligand for dsRNA as binding to the same sequences of dsDNA is at least an order of magnitude weaker. Conjugation of PNA with short lysine peptides further enhances binding affinity and RNA over DNA selectivity without compromising sequence selectivity of the triple helix formation. Preliminary results suggest that the modified PNAs can bind and recognize noncoding dsRNAs through the triple helix formation. The cationic nucleobase and backbone (Lys) modifications enhance the cellular uptake of PNA. Thus, modified PNAs may be promising compounds for detecting and interfering with the function of biologically relevant dsRNA in live cells.