SELEX revealed a variety of DNA aptamers and catalytic DNA known as DNAzymes (or Deoxribozymes). Breaker and Joyce selected the first DNAzyme, a RNA-cleaving DNA.breaker1994 In 1997 Santoro and Joyce describe the 7-18 and 10-23 DNAzyme santoro1997 which since then have been of special interested in DNAzyme research. Both recognize their substrate RNA by Watson-Crick base pairing and catalyze the attack of a 2’ hydroxyl group that leads to the formation of a 2’,3’-cyclic phosphate and leaves a 5’ hydroxyl RNA terminus.santoro1998 Their activity has also been engineered to be dependent on the presence of a small molecule by the addition of an aptamer to its substrate recognition site.Wanga2002Wangb2002 To verify the prediction of the software we fused the calculated aptamers to a DNAzyme and thus created a ligand dependent activity.
For this we used the HRP-mimicking DNAzyme which was described in 1998.Travascio1998 It folds into a G-quadruplex that forms a complex with hemin and is then able to mimic the activity of a horse raddish peroxidase. Hence it is capable to produce reactive oxygen species (ROS) by the reduction of hydrogen peroxide to water. These ROS then leads to an activation of luminol which then becomes chemiluminescent. In several of our subprojects we exploit this function as an easy readout such as for the AptaBody.