Switchable Triggered Interconversion and Reconfiguration of DNA Origami Dimers and Their Use for Programmed Catalysis

The switchable reconfiguration of a mixture of two dimers of DNA origami tiles, AB and CD, into a mixture of two DNA origami dimers composed of AD and CB, using a collection of fuel and antifuel strands, is presented. The reversible reconfiguration of the mixture of dimers AB and CD into AD and CB, is followed by labeling each of the tiles with 0, 1, 2, and 3 4× hairpins labels and by imaging the dimer structures by atomic force microscopy. Subjecting the reconfigurable dimer mixtures to a collection of Mg²⁺-ion-dependent DNAzyme subunits and the substrates consisting of the ROX/BHQ2-modified substrate and the FAM/BHQ1-modified substrate leads to the triggered and programmed switchable operation, in the presence of appropriate fuel and antifuel strands. In the presence of the AB and CD mixture, the DNAzyme subunits cleaving the ROX/BHQ2-modified substrate is switched on, leading to the fluorescence of ROX. The reconfiguration of the AB and CD dimer mixture to the AD and CB dimer mixture leads to the assembly of the DNAzyme subunits that switches on the cleavage of the FAM/BHQ1-modified substrate and to the fluorescence of FAM. By the cyclic and reversible reconfiguration of the AB and CD dimer mixture to the AD and CB dimer mixture, in the presence of the appropriate fuel and antifuel strands, the switchable catalytic operation of two Mg²⁺-ion-dependent DNAzymes, leading to the fluorescence of ROX or FAM, is demonstrated.