Enzyme-Powered Three-Dimensional DNA Nanomachine for DNA Walking, Payload Release, and Biosensing

Abstract

Herein, we report a DNA nanomachine, built from a DNA-functionalized gold nanoparticle (DNA-AuNP), which moves a DNA walker along a three-dimensional (3-D) DNA-AuNP track and executes the task of releasing payloads. The movement of the DNA walker is powered by a nicking endonuclease that cleaves specific DNA substrates on the track. During the movement, each DNA walker cleaves multiple substrates, resulting in the rapid release of payloads (predesigned DNA sequences and their conjugates). The 3-D DNA nanomachine is highly efficient due to the high local effective concentrations of all DNA components that have been co-conjugated on the same AuNP. Moreover, the activity of the 3-D DNA nanomachine can be controlled by introducing a protecting DNA probe that can hybridize to or dehybridize from the DNA walker in a target-specific manner. This property allows us to tailor the DNA nanomachine into a DNA nanosensor that is able to achieve rapid, isothermal, and homogeneous signal amplification for specific nucleic acids in both buffer and a complicated biomatrix.

A microRNA-initiated DNAzyme motor operating in living cells

“…2). Similar to other DNA motors that use DNA tracks built on nano- and micro-materials83031, walking of the DNAzyme motor along the AuNP is stochastic.…”

“…DNA origami was further used to construct two-dimensional tracks, increasing the walking steps and directionality of the motor262728. Recently, DNA tracks were built on nano- and micro-materials, including gold film7, microparticles8, carbon nanotubes1029 and gold nanoparticles (AuNPs)3031, further improving the mobility and processivity of the DNA motors. Instructional strands were included precisely at specific positions of DNA tracks, enabling control of the walking direction of the motors2232.…”

Enzyme Catalysis To Power Micro/Nanomachines

“…The motion is controlled by cyclic reactions of hybridization and hydrolysis between the DNA-based motor and the track, recurring to restriction enzymes that comprehend specific recognition sites in the hybridized motor–track complex. 11−13,51−54 …”

“…Li and co-workers 54 engineered a patterned track and DNA walker conjugated onto the same spherical particle, which increased local effective concentrations of DNA. This motor achieves motion through the hybridization of the walker with the DNA substrate, followed by hydrolysis by a nicking endonuclease.…”

DNA Nanobiosensors: An Outlook on Signal Readout Strategies

“…Such stimuli responsive structures can be not only used as biosensors but also configured to react to specific biomarkers and release cargos from macromolecular containers [63]. For example, a recent enzyme-powered DNA-AuNP nanomachine was used to release payloads while also serving as a biosensor for nucleic acid detection [64]. Such nanostructures that can act according to stimuli can be used as "sense-and-treat" devices for theranostic applications [65].…”