“Not unlike molecular machines that operate autonomously, an important type of synthetic molecular machine is designed to respond to commands from the outside,” explains team leader Eyal Nir of the Ben-Gurion University of the Negev in Beer Sheva. “These commands often come in the form of chemical compounds. To communicate with such machines, we need an efficient method for providing and removing chemical commands to and from the machine environment and a method to observe the machine state during assembly and operation. We have succeeded in doing just that using a microfluidic-based platform and single-molecular fluorescence spectroscopy.

“Microfluidics is a technology based on the flow of solutions in sub-microlitre volumes, which allows us to precisely introduce and remove chemicals into and out of synthetic molecular machines,” he adds. “Single-fluorescence spectroscopy allows us to observe the state of individual machines during operation with nanometre and sub-second resolution.”

Inspired by the kinesin motor protein

Like previous such bipedal walkers, the device made by Nir and colleagues was inspired by the kinesin motor protein found in nature that is powered by the hydrolysis of adensone triphosphate (ATP). This motor can take hundreds of steps per second before it dissociates from a microtubule filament. For such walkers, the trailing “leg” must somehow “know” not to detach itself from the track before the leading leg is stably anchored.

“Our motor has two legs made from DNA strands and walks by taking tiny 11 nm-sized steps that involve its legs tethering and untethering to the pre-defined DNA track (which is also made from DNA using a technology called DNA origami),” explains Nir. “It is powered by different ‘fuel’ and ‘anti-fuel’ DNA strands (provided by the external microfluidic platform) that push it along.

First computer-controlled DNA molecular machine

“The walkers can take 32 steps, corresponding to 64 different chemical reactions, and walk a distance of more than 370 nm, including three changes in direction,” he tells nanotechweb.org. “We command each of these and the changes in direction by a pre-programmed computer algorithm.”

This is the first DNA molecular machine that is controlled by a computer, he says, and more importantly, the first controlled molecular machine in which the redundant and used chemical commands are automatically washed away after use. This allows the machine to continuously operate undisrupted while remaining in its preferred environment.

Next steps for nanomachines

According to the researchers, the new technology should allow DNA motors and machines, such as DNA computers, mechanical nano-manipulators and nano-factories for molecular assembly, to be externally controlled using minute flows of fluid. It should thus help in the development and improvement of complex machines that perform a variety of tasks on the molecular level.

The team, reporting its work in ACS Nano DOI: 10.1021/acsnano.7b00547, says that it is now busy developing a new type of bipedal walker capable of taking a much larger number of steps – possibly hundreds-to-thousands – and at much greater speed. “We are also fabricating a rotary motor that will be able to rotate at high speeds without stalling, and are working on a system that consists of several independent motors that can efficiently transfer molecular cargo between them,” reveals Nir.