DNA Helix-stack Switching as the Basis for the Design of Versatile Deoxyribonsensors

The charge conduction properties of deoxyribonucleic acids (DNA) can be harnessed for monitoring the binding of a ligand to its receptor. Here, we show how DNA-based sensors (deoxyribosensors) consisting of a photo-activated oxidant tethered to a receptor-containing DNA molecule can be used to monitor the presence of a ligand. Phosphorescence measurements, reflective of changes in charge conduction to a targeted region in these deoxyribosensors are made in the presence and absence of the test ligand. The deoxyribosensors described here, exploit established rules for DNA helical stacking in three-way junctions and use previously selected aptamer sequences as receptors for target analytes. More specifically, a systematic investigation outlining the characteristics of a deoxyribosensor for the detection of the amino acid derivative, argininamide are presented. These results suggest a general design for deoxyribosensors for any molecular ligand for which an aptamer sequence can be obtained. Also, a new methodology for investigating helical stacking of nucleic acids of unknown tertiary structure, such as DNAzymes or RNAzymes is discussed.