Aptaswitch/aptakiss adenosine sensor design based on the selection of new DNA/DNA kissing complexes

Abstract

Kissing complexes involve interactions between complementary loops of two RNA hairpins. These complexes are continously found in RNA structures and are essential for several biological processes, including the dimerization of retroviral RNA genomes, regulation of plasmid copy number, and small RNA-based control of mRNA translation. We previously identified novel RNA-RNA and RNA-DNA kissing complexes through the in vitro selection of oligonucleotides from synthetic libraries. In order to expand the use of kissing complexes to aptamers and DNA nanotechnology, we describe the selection and characterization of DNA-DNA kissing complexes and their application in the development of DNA adenosine aptasensors. Four DNA/DNA kissing complexes were identified from SELEX and characterized by EMSA and fluorescence anisotropy. The couple dk25/dk26 was further modified to generate an adenosine-triggered aptaswitch, where the addition of adenosine selectively induces the dissociation of loop-loop interactions. This paves the way for a new class of nucleic acid modules, which could be useful for the design of controlled nanostructure assembly and disassembly.