A synthetic DNA motor that transports nanoparticles along carbon nanotubes

Abstract

Intracellular protein motors have evolved to perform specific tasks critical to the function of cells such as intracellular trafficking and cell division. Kinesin and dynein motors, for example, transport cargoes in living cells by walking along microtubules powered by adenosine triphosphate hydrolysis. These motors can make discrete 8 nm centre-of-mass steps and can travel over 1 µm by changing their conformations during the course of adenosine triphosphate binding, hydrolysis and product release. Inspired by such biological machines, synthetic analogues have been developed including self-assembled DNA walkers that can make stepwise movements on RNA/DNA substrates or can function as programmable assembly lines. Here, we show that motors based on RNA-cleaving DNA enzymes can transport nanoparticle cargoes-CdS nanocrystals in this case-along single-walled carbon nanotubes. Our motors extract chemical energy from RNA molecules decorated on the nanotubes and use that energy to fuel autonomous, processive walking through a series of conformational changes along the one-dimensional track. The walking is controllable and adapts to changes in the local environment, which allows us to remotely direct 'go' and 'stop' actions. The translocation of individual motors can be visualized in real time using the visible fluorescence of the cargo nanoparticle and the near-infared emission of the carbon-nanotube track. We observed unidirectional movements of the molecular motors over 3 µm with a translocation velocity on the order of 1 nm min(-1) under our experimental conditions.

Controlling Motion at the Nanoscale: Rise of the Molecular Machines

“…89,90 In a more recent example, Choi and coworkers described the fueled, autonomous translocation of CdS nanocrystal cargo by a single-stranded RNA-cleaving DNA enzyme over 3 µm along a RNA-decorated carbon-nanotube track while demonstrating robust control over stopping and starting the walker ( Figure 6). 91 These proof-of-principle designs for DNA walkers show promise for DNA-based circuits, nanorobotics, and cargo transport, supported by quantitative control over rates for complementary strand displacement reactions. 92,93 Still, these complicated mechanical systems have generally been plagued by slow kinetics and poor overall performance.…”

Design Principles of DNA Enzyme-Based Walkers: Translocation Kinetics and Photoregulation

“…The reaction pathway of a single walking cycle or a single turnover event of DNA and nicking restriction enzymes was proposed as a 4-step process 18,30,34 . However, three rate-limiting intermediate steps in the single turnover event predominantly determine the overall walker kinetics.…”

“…The synthesized CdS nanoparticle has a diameter of ~3 nm and an emission peak at 550 nm. Approximately 20 DNA enzyme molecules are estimated per CdS nanoparticle 34,43 . It should be noted that only one DNA enzyme is involved in walking operation.…”

“…To elucidate the effect of the catalytic core type alone, the lengths of the upper and lower recognition arms were fixed at 7 and 16, respectively, and the measurements were carried out under identical conditions: pH 8.0 and 25 °C in TAE buffer with Mg 2+ . To visualize individual motor translocation, we spectroscopically tracked a walker-integrated CdS quantum dot along an immobilized carbon nanotube which fluoresce in the visible and near-infrared, respectively (see Figures S2-S50) 34 . Figure 3a shows experimentally obtained motor speeds (filled objects) and calculated single turnover rates (solid curves in the corresponding colors) of the enzymatic walkers as a function of Mg 2+ concentration.…”

Peptide–Metal Organic Framework Swimmers that Direct the Motion toward Chemical Targets

“…[16][17][18] The artificial walkers consisting of DNA and microtubule systems were demonstrated to be guided to specific locations along tracks pre-patterned on substrates and capture targets without sensing. [19][20][21][22] Thus, these chemical walkers are limited to capture targets only when targets are deposited on the track of guided motion, which is not a practical condition for the detection of target molecules in unknown locations. Ideal chemical motors can freely move in solution and then sense and directionally swim toward targets.…”