Mechanisms, Methods of Tracking and Applications of DNA Walkers: A Review

Abstract

In recent years, DNA nanotechnology expanded its scope from structural DNA nanoarchitecture towards designing dynamic and functional nanodevices. This progress has been evident in the development of an advanced class of DNA nanomachines, the so‐called DNA walkers. They represent an evolution of basic switching between distinctly defined states into continuous motion. Inspired by the naturally occurring walkers such as kinesin, research on DNA walkers has focused on developing new ways of powering them and investigating their walking mechanisms and advantages. New techniques allowing the visualization of walkers as single molecules and in real time have provided a deeper insight into their behavior and performance. The construction of novel DNA walkers bears great potential for applications in therapeutics, nanorobotics or computation. This review will cover the various examples and breakthrough designs of recently reported DNA walkers that pushed the limits of their performance. It will also mention the techniques that have been used to investigate walker nanosystems, as well as discuss the applications that have been explored so far.

DNA Gold Nanoparticle Motors Demonstrate Processive Motion with Bursts of Speed Up to 50 nm Per Second

“…Nanomachines are ubiquitous in nature. , For example, the kinesin motors travel micrometer length distances on microtubules with nm/s velocities by hydrolyzing ATP . Recapitulating the properties of these biological motors in synthetic systems has been a long-standing goal as these synthetic systems hold promise in the development of next generation sensors, molecular computers, and drug delivery platforms. − …”

Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective

“…Recently, they reported a DNA scaffold-based voltmeter that can report the membrane potential of organelles, Voltair (Saminathan et al, 2021). DNA walkers, which can locomote along programed tracks through the processes including DNA strand hybridization, enzymatic cleavage of DNA strands, and DNA strand displacement, are among the most studied dynamic DNA nanodevices, and have been broadly used in various practical applications, such as biosensing, in recent years (Valero and Skugor, 2020;Cha et al, 2015). Dong et al developed a highly sensitive electrochemical method for the detection of tumor exosomes (Dong et al, 2018).…”

Advances in Designer DNA Nanorobots Enabling Programmable Functions

“…[29b] Therefore, by integrating the enzyme-based power unit and cascaded strand displacement reactions, the DNA nanorobot can be customized to perform continuous actuation, realizing self-sensing and selfexecuting mechanical operations for desired functions. [37] 3. Designer DNA Nanorobots Performing Desirable Biomedical Functions…”

“…[53] Continuously actuating DNA nanorobots such as DNA walkers or motors can execute a series of autonomous molecular operations to accomplish complicated molecular tasks. [34,37,54] The directional mechanical movement of DNA walkers could be powered by nucleic acid hybridization (e. g. toehold-mediated strand displacement and catalytical hairpin assembly), hydrolysis of the track catalyzed by various enzymes, such as exonuclease, nicking endonuclease, RNase H, or DNAzymes, [38b,43,58] and light. [24a,55] With enzyme-based hydrolysis of the track, various "burnt-bridge" DNA walkers have been developed to autonomously locomote along a designed route without repeated manual interventions.…”