Nonionic side chains modulate the affinity and specificity of binding between functionalized polyamines and structured RNA.

This Communication introduces side-chain-bearing polyamines as molecules for selective recognition of folded RNA structures. The complex folded structures associated with RNA create binding pockets for proteins, and also binding sites for small molecules. Developing organic molecules that can bind RNA with high affinity and specificity is a challenge that must be overcome for RNA to be considered a viable drug target. In this work, six polyamines with different side chains were synthesized to test for effects on binding affinity and specificity to TAR RNA and RRE RNA of HIV. Binding interactions between polyamines and RNAs were examined using two footprinting assays, based on terbium-induced cleavage and magnesium-catalyzed cleavage at higher pH. The binding constants and the binding specificity were highly dependent on the side chains of the polyamines, demonstrating that this class of molecules is a very promising starting point for development of highly selective RNA-binding ligands.