Design of a β-hairpin peptide-intercalator conjugate for simultaneous recognition of single stranded and double stranded regions of RNA

Designing receptors that bind RNA is a challenging endeavor because of the unique and sometimes complex structure of RNA. However these structural features provide regions for ligands to bind using different types of interactions. To increase specificity and binding affinity to RNA, divalent systems have been designed which incorporate more than one binding motif into one molecule. Using this approach, we have designed a two part heteroconjugate, WKWK-Int, which contains a β-hairpin peptide covalently linked to an RNA intercalator. This heteroconjugate was designed to bind duplex RNA through intercalation and simultaneously interact with a single stranded bulge region using the side chains of the β-hairpin peptide. We have used fluorescence anisotropy experiments to show that the heteroconjugate has an increased binding affinity over either one of the individual ligands. Additionally, RNase footprinting experiments show that the structure of the peptide is necessary for the protection of one particular base in the RNA bulge region. When tested against other RNA molecules containing a stem-bulge structure, the designed heteroconjugate was found to be specific for this RNA sequence. This work provides evidence that the covalent linkage of two weak RNA ligands can greatly increase the binding affinity and also provide specificity to the binding event.