Deoxystreptamine dimers bind to RNA hairpin loops.

RNA is known to have multiple roles in critical cellular functions. Thus, there is great potential for RNA-binding small molecules as both therapeutic agents and cellular probes. Unfortunately, the multiple secondary structures that RNA can adopt have caused difficulty in the development of a general paradigm for RNA-small molecule binding. In particular, the standard RNA-binding compounds such as aminoglycosides do not generally bind RNA hairpin loops, a widespread and vitally important secondary structural motif. In this manuscript we report that dimers of deoxystreptamine bind to RNA hairpin loops with affinities rivaling that of RNA-aminoglycoside interactions.