A homodimer interface without base pairs in an RNA mimic of red fluorescent protein

Corn, a 28-nucleotide RNA, induces yellow fluorescence of its cognate ligand (3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime, DFHO) by >1000-fold. It was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer. Unusually, the dimer interface, where six unpaired adenosines break overall 2-fold symmetry, lacks any intermolecular base pairs. The homodimer encapsulates one DFHO at its inter-protomer interface, sandwiching it with a G-quadruplex from each protomer. Corn and the green-fluorescent Spinach RNA are structurally unrelated. Their convergent use of G-quadruplexes underscores the usefulness of this motif for RNA-induced small-molecule fluorescence. The asymmetric dimer interface of Corn could form the basis for the development of mutants that only fluoresce as heterodimers. Such variants would be analogous to Split GFP, and may be useful in analyzing RNA co-expression or association, or in designing self-assembling RNA nanostructures.