Nucleic acid nanotechnology

Abstract:

Intelligent nanomechanical devices that operate in an autonomous fashion are of great theoretical and practical interest. Recent successes in building large scale DNA nano-structures, in constructing DNA mechanical devices, and in DNA computing provide a solid foundation for the next step forward: designing autonomous DNA mechanical devices capable of arbitrarily complex behavior. One prototype system towards this goal can be an autonomous DNA mechanical device capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical design and prototype experimental construction of an autonomous unidirectional DNA walking device moving along a linear track, we present here the design of a nanomechanical DNA device that autonomously mimics the operation of a 2-state 5-color universal Turing machine. Our autonomous nanomechanical device, called an Autonomous DNA Turing Machine (ADTM), is thus capable of universal computation and hence complex translational motion, which we define as universal translational motion.

Abstract:

Imagine a host of nanoscale DNA robots move,autonomously over a microscale DNA nanostructure, each following a programmable route and serving as a nanoparticle and/or an information carrier. The-accomplishment of this goal has many applications in nanorobotics, nano-fabrication, nano-electronics, nano-diagnostics/therapeutics, and nano-computing. Recent success in constructing large scale DNA nanostructures in a programmable way provides the structural basis to meet the above challenge. The missing link is a DNA walker that can autonomously move along a route programmably embedded in the underlying nanostructure - existing synthetic DNA mechanical devices only exhibit localized non-extensible motions such as bi-directional rotation, open/close, and contraction/extension, mediated by external environmental changes. We describe in this paper two designs of autonomous DNA walking devices in which a walker moves along a linear track unidirectionally. The track of each device consists of a periodic linear array of anchorage sites. A walker sequentially steps over the anchorages in an autonomous unidirectional way. Each walking device makes use of alternating actions of restriction enzymes and ligase to achieve unidirectional translational motion.