A bipedal DNA Brownian motor with coordinated legs

A significant challenge in engineering molecular motors is designing mechanisms to coordinate the motion between multiple domains of the motor so as to bias random thermal motion. For bipedal motors, this challenge takes the form of coordinating the movement of the biped's legs, so they can move in a synchronized fashion. To address this problem, we have constructed an autonomous DNA bipedal walker that coordinates the action of its two legs by cyclically catalyzing the hybridization of metastable DNA fuel strands. This process leads to a chemically ratcheted walk along a directionally polar DNA track. By covalently crosslinking aliquots of the walker to its track in successive walking states, we demonstrate that this Brownian motor can complete a full walking cycle on a track whose length could be extended for longer walks. We believe this study helps to uncover principles behind the design of unidirectional devices that can function without intervention. This device should be able to fulfill roles that entail the performance of useful mechanical work on the nanometer scale.;This dissertation begins with a brief introduction to DNA nanotechnology and past efforts to make walking systems out of DNA. A detailed description of the system we designed is then given. The last sections include a history of how the design evolved and general design principles that were learned in the process of making the device. Some prospects for improving and extending the design are also presented. It concludes with a "take away message" about designing Brownian motors.