A Free‐Running DNA Motor Powered by a Nicking Enzyme

Abstract

Herein, we present a simple linear motor, built from DNA and a restriction enzyme, which moves a DNA cargo in discrete steps along a DNA track. Movement is powered by a nicking enzyme that cuts the track. Damage to the track in the wake of the cargo imposes directionality.The specificity of base-pairing, the rigidity of short segments of the double helix, and the flexibility of singlestranded segments make DNA an ideal material for construction of nanometer-sized mechanical devices. [1][2][3][4][5][6][7] Such devices can generate forces of the order of picoNewtons, [2] in the same range as the forces developed by single-molecule

The effect of topology on the structure and free energy landscape of DNA kissing complexes

“…We are also confident of the general robustness of the model, based on the wide range of DNA systems on which we 19,34,35 and others 38 have tested the model. These so far include DNA nanotweezers, 33 "burnt bridges", 39 and two-footed 40 DNA walkers, as well as processes such as DNA displacement, 41 overstretching, 42 cruciform formation, 43 and the formation of liquid crystalline phases. 44 However, we should also note that the model does introduce a significant level of coarse graining and neglects several features of the DNA structure and interactions.…”

Sequence-dependent thermodynamics of a coarse-grained DNA model

“…1 Given the reliability and programmability of base-pair formation, DNA is an obvious candidate for use in self-assembly. Indeed, DNA has been exploited as a building block for the assembly of nanostructures and active devices: successes include DNA computation, 2 motors, 3,4 hierarchical self-assembly of tiles, 5 and self-assembly of strands into large structures such as DNA origamis. 6 Many theoretical and computational approaches have been developed to study DNA.…”

A nucleotide-level coarse-grained model of RNA

“…3 DNA nanotechnology 4 uses DNA molecules to create nanoscale structures and active devices. Examples of experimentally realized systems include DNA motors, 5,6 selfassembled nanostructures such as DNA origamis 7 and the use of DNA strands for computation. 8 Since RNA molecules are more difficult to handle and preserve than DNA in experimental settings, developing RNA-based nanodevices has been a more challenging task.…”