Structural characterization of a flavin-specific RNA aptamer by chemical probing

In a previous study, an RNA aptamer for the specific recognition of flavin cofactors was isolated from a combinatorial RNA-pool. We have now carried out a structural analysis of this RNA by chemical probing and identified residues protected from modification in the presence of the cofactor and modifications that interfere with its complexation. An induced fit of the RNA motif occurs upon cofactor binding. Our analysis led to a refined secondary structure model for the FMN/RNA complex.