Preferred RNA Binding Sites for a Threading Intercalator Revealed by In Vitro Evolution Original Research Article

In pursuit of small molecules capable of controlling the function of RNA targets, we have explored the RNA binding properties of peptide-acridine conjugates (PACs). In vitro evolution (SELEX) was used to isolate RNAs capable of binding the PAC Ser-Val-Acr-Arg, where Acr is an acridine amino acid. The PAC binds RNA aptamers selectively and with a high degree of discrimination over DNA. PAC binding sites contain the base-paired 5′-CpG-3′ sequence, a known acridine intercalation site. However, RNA structure flanking this sequence causes binding affinities to vary over 30-fold. The preferred site (KD = 20 nM) contains a base-paired 5′-CpG-3′ step flanked on the 5′ side by a 4 nt internal loop and the 3′ side by a bulged U. Several viral 5′- and 3′-UTR RNA sequences that likely form binding sites for this PAC are identified.