DNA Bipedal Motor Achieves a Large Number of Steps Due to Operation Using Microfluidics-Based Interface

Abstract

Realization of bioinspired molecular machines that can perform many and diverse operations in response to external chemical commands is a major goal in nanotechnology, but current molecular machines respond to only a few sequential commands. Lack of effective methods for introduction and removal of command compounds and low efficiencies of the reactions involved are major reasons for the limited performance. We introduce here a user interface based on a microfluidics device and single-molecule fluorescence spectroscopy that allows efficient introduction and removal of chemical commands and enables detailed study of the reaction mechanisms involved in the operation of synthetic molecular machines. The microfluidics provided 64 consecutive DNA strand commands to a DNA-based motor system immobilized inside the microfluidics, driving a bipedal walker to perform 32 steps on a DNA origami track. The microfluidics enabled removal of redundant strands, resulting in a 6-fold increase in processivity relative to an identical motor operated without strand removal and significantly more operations than previously reported for user-controlled DNA nanomachines. In the motor operated without strand removal, redundant strands interfere with motor operation and reduce its performance. The microfluidics also enabled computer control of motor direction and speed. Furthermore, analysis of the reaction kinetics and motor performance in the absence of redundant strands, made possible by the microfluidics, enabled accurate modeling of the walker processivity. This enabled identification of dynamic boundaries and provided an explanation, based on the "trap state" mechanism, for why the motor did not perform an even larger number of steps. This understanding is very important for the development of future motors with significantly improved performance. Our universal interface enables two-way communication between user and molecular machine and, relying on concepts similar to that of solid-phase synthesis, removes limitations on the number of external stimuli. This interface, therefore, is an important step toward realization of reliable, processive, reproducible, and useful externally controlled DNA nanomachines.

Tunable DNA Origami Motors Translocate Ballistically Over μm Distances at nm/s Speeds

“…Alternatively, Nir et al. sacrificed autonomy of bipedal DNA walkers to gain processivity, increasing the number of steps from 7 to 32 (44 % percent of the walkers) . Increasing the number of DNA legs to create polyvalent DNA motors can also boost processivity at the cost of diminished speed.…”

“…DNA origami has been instrumental in the field of dynamic DNA nanotechnology. In fact, the vast majority of DNA motors use DNA origami as their track . Patterning the location of fuel footholds on an origami scaffold is also a common strategy to guide motor trajectory .…”

“…In fact, the vast majority of DNA motors use DNA origami as their track . Patterning the location of fuel footholds on an origami scaffold is also a common strategy to guide motor trajectory . Herein, we aimed to test the hypothesis that DNA origami structures can be engineered as the body for a polyvalent DNA motor.…”

DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences

“…Numerous current works regarding the machine-assisted production and analysis of small-molecule compounds, [70] DNAm olecules, [71] colloidal nanoparticles, [72] and technical platforms for handling and analysis of DNA nanostructures [73] and DNAs urfaces [23,74] indicate that the development of integrated systems involves lab-on-a-chip devices and robotics along with in-line analytics and data acquisition. Numerous current works regarding the machine-assisted production and analysis of small-molecule compounds, [70] DNAm olecules, [71] colloidal nanoparticles, [72] and technical platforms for handling and analysis of DNA nanostructures [73] and DNAs urfaces [23,74] indicate that the development of integrated systems involves lab-on-a-chip devices and robotics along with in-line analytics and data acquisition.…”

Stimuli‐Responsive DNA Self‐Assembly: From Principles to Applications

“…[48] By developing am icrofluidics-based user interfacet of acilitate the handling of multiple DNA inputs and the removal of redundant strands, Nir and co-workersa chieved al arge number of consecutive movements teps of aD NA bipedal walker. [49] They also conducted an experimental and theoretical study to investigate the influence of step size on the walking efficiency and stepping kinetics of the DNA bipedal motor. [50] Beyondw alking alongp rescribed tracks, Qian and co-workers built aD NA nanorobot capable of random walkinga nd smart cargo sorting on at wo-dimensional DNA origami land.…”