Harnessing thiophilic cadmium to enhance 8-17 DNAzyme activity in cascade oligo biosensors

DNAzymes are metal-dependent catalysts with vast potential for therapeutic and diagnostic applications. Herein, optimization of the performance of a commercial laboratory fluorescence resonance energy transfer (FRET) biosensor, that is currently used to detect, with 1 fM sensitivity, the ompA gene of Chlamydia trachomatis, is considered through the addition of 20-40 μM of Cd²⁺ to model biosensors. Up to 10-fold signal enhancement is observed in pertinent solution-based sensing formats based on 8-17 DNAzyme, the mechanism of which is determined using molecular-mechanics simulations of the operation of its catalytic site. In contrast, only minor improvements are predicted and observed using 10-23 DNAzyme as the catalyst. These results are then translated to yield a three-fold increase in sensitivity for a close-model two-chamber biosensor that involves bead-bound DNAzymes. Thiolated linkages are used to bind the DNAZymes to the beads, with thiophilic Cd²⁺ shown to restrain 75 % of possibly detached oligos, with no unwanted background signal detected that could be attributed to detached oligos during biosensor operation.