A Programmable Target-Initiated DNAzyme Walker Walking along a Spatially Isolated and Highly Hybridizable Substrate Track on Nanoparticle Surface.

Synthetic DNA machines that operate on the nanoscale three-dimensional (3D) track have attracted rapidly increasing interest because of their potential in biocomputing, drug delivery, and biosensing applications. Current nanoscale 3D DNA tracks are typically created by self-assembling thiolated oligonucleotides at gold nanoparticles (AuNPs) surface via the strong Au-S chemistry. However, it remains challenging to precisely control the orientation and conformation of 3D DNA track on AuNPs surface and finely tune the hybridization ability of 3D track. Herein we report for the first time a poly adenine (polyA)-based, spatially isolated 3D DNA track, on which a target-initiated DNAzyme walker moves by a burnt-bridge mechanism with improved efficiency and processivity. PolyA serves as an anchoring block for preferential binding with the AuNPs surface, and the appended substrate block adopts an upright conformation that favors hybridization and DNAzyme-mediated cleavage. The operation of this target-initiated DNAzyme walker was monitored in real time and at the single-particle level. We tested the cleavage efficiency of 3D substrates with various polyA block lengths, which displayed that the DNAzyme activity was remarkably improved as compared to thiol-based 3D track. We also explored bioanalytical applications of this DNAzyme nanomachine by movement-triggered cascade signal amplification.