A signal amplifier engineered via a cleavable stochastic bipedal DNA walker

Abstract

Bipedal DNA walkers (BDWs) are highly efficient signal amplifiers for biomolecular analysis but are of limited activation strategies for non-nucleic acid targets. Herein, we report a cleavable BDW design that effectively expands the target sets of this class of signal amplifiers. Specifically, we first demonstrated that folded DNA structures at the 3` end of BDW are highly efficient steric blockers capable of fully deactivating 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 enriches the design rules for engineering DNA nanomachines as highly efficient biosensors.