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

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. [Copyright &y& Elsevier]