Computer Controlled Fast and Processive DNA Bipedal Walker

Biological molecular machines can perform hundreds of serial operations with remarkably high yields and operational rates. Inspired by such machines, researchers have develop synthetic DNA-based machines and demonstrate enzymatic activity, structural manipulations, maneuvering of substrate molecules and molecular computing. However, low operational yields and slow machine responds hinder development and application.

We have developed a fast and efficient DNA bipedal motor that strides on a DNA origami. The motor operates by responding to `fuel` and `antifuel` DNA strands that are provided by computer controlled microfluidics device, and the motor operation and progress are monitored by single-molecule fluorescence spectroscopy.

We demonstrate the performance of 32 walking steps (64 consecutive chemical reactions), which amount to 370 nanometers traveled by the walker. In this motor version, high concentrations of fuel strands, which are required for fast motor respond, resulted in low operational yields. To solve this problem, we further developed a bipedal walking mechanism that allows using high concentrations of fuels without reducing operational yield, and demonstrated more then 10-fold increase in motor speed. This is significantly more operations and faster motor responds than were previously reported for DNA based externally controlled molecular machines.

Detailed analysis of the motor performance and reaction kinetics, made possible by the microfluidics and single-molecule fluorescence, yielded detailed understanding of the motor operational mechanisms and accurate modeling of the walker processivity and its dependence on step size, and facilitate rational improvements of the motor design and of its operation mechanism.