The interaction between the RNA aptamer Dap1 and DasR mirrors DNA operator site recognition in GntR repressors

RNA aptamers targeting bacterial repressors show significant promise in synthetic biology. We determined the crystal structure of the SELEX-derived aptamer Dap1 in complex with its target, the GntR/HutC repressor family member DasR. In the complex, two monomers of Dap1 individually sequester the two DNA-binding domains (DBDs) of the dimeric repressor. The DBDs of DasR interact with Dap1 in a highly similar fashion to what is observed in GntR-dsDNA complexes. This also holds true at the level of single amino acids, and identical arginine residues play crucial roles in both RNA and DNA recognition. The structure shows how DasR binding to Dap1 competes with DasR binding to its operator dre sites and, hence, how Dap1 is able to induce DasR-controlled gene transcription in vivo. A structure-informed Dap1 aptamer pool randomized at only four positions allowed for the identification of the novel aptamer Dap1m1 that binds and de-represses the DasR homologous protein NagR instead of DasR. This shows that the complex structure can serve as a blueprint for the design of novel aptamer-protein interaction pairs, opening up new venues for the generation of aptamers directed against other GntR/HutC family members and possibly also against other repressor classes.