Kissing complex-based aptaswitches.
Jean-Jacques Toulmé1,2, Eric Dausse1, Guillaume Durand1,3, Corinne Ravelet4, Eric Peyrin4, Laurent Azéma1.
1, ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, France
2, Novaptech, Pessac, France
3, Present address : Department of Nutrition, Health, and Agricultural Sector, Bordeaux Sciences Agro, Gradignan, France
4, Department of Molecular Pharmacology, University Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Saint-Martin d’Hères, France
Kissing interactions result from the formation of Watson-Crick base pairs between complementary loops of RNA hairpins. Such complexes were demonstrated to regulate various steps of gene expression. Long ago we demonstrated that SELEX against RNA hairpins leads to the selection of aptamers organized themselves as hairpins interacting with the target through loop-loop base-pairing. Such complexes were shown to artificially control viral gene expression.
We took advantage of the properties of kissing complexes for designing aptasensors: aptamers organized as imperfect hairpins were engineered for switching from an unfolded to a folded shape upon binding to the cognate ligand. The apical loop of the folded aptamer is secondarily specifically recognized by a short RNA hairpin called aptakiss through loop-loop interactions. The formation of the aptaswitch-aptakiss complex signals the presence of the ligand.
We characterized RNA-RNA, RNA-DNA and DNA-DNA kissing complexes from a wide repertoire of kissing motifs. We engineered several aptaswitches using various kissing motifs for the detection of purine analogues. Our aptaswitches allow multiplex analysis either on biochip or in solution with different signals (SPR, fluorescence, etc…).