A signal amplifier engineered with a cleavable stochastic bipedal DNA walker

Abstract

Bipedal DNA walkers (BDWs) are highly efficient signal amplifiers for nucleic acid analysis. So far, there are very limited activation strategies for non-nucleic acid targets. Herein, we report a design involving a cleavable BDW that effectively expands the set of targets of this class of signal amplifiers. Specifically, we demonstrated that folded DNA structures at the 3′ end of a BDW are highly efficient steric blockers capable of fully deactivating the BDW. Using a RNA-cleaving DNAzyme serving both as a steric blocker and a target cleavable motif, we successfully engineered a signal amplifier for uranyl ions with a limit of detection at 1.0 nM. Our study provides additional design rules for engineering DNA nanomachines as highly efficient biosensors.