NANO: EMT: A DNA-Based Autonomous Programmable Molecular Transport Network

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There has been considerable recent progress demonstrating a class of DNA molecular-effectors called "DNA walkers" that execute various forms of biped locomotion along self-assembled linear DNA nanostructures. In particular, the walker constructed by Reif's group at Duke is the ?rst DNA walker that executes autonomously, without external intervention. This project will extend the emerging nanotechnology of DNA walkers to provide a programmable network system for molecular transport and communication within self-assembled DNA lattices. Our system will perform a set of communication and transport operations. These include, among other things, the ability to (i) perform a class of ?nite state operations on the information provided by speci?ed sites of the 2D lattice, (ii) route ?nite state information and/or nanoparticles to and from pairs of tiles of the DNA lattice or to other specified sites. Although the degree of programmability of the proposed constructs is restricted to ?nite state transitions, still the programmability far exceeds current experimental demonstrations of current molecular effectors and molecular-motor devices. We intend to make significant improvements to Duke's existing autonomous DNA walkers to allow them to have far more impact to nanoscience and nanotechnology, including extending the DNA walkers to be programmable in at least two senses: (a) They will be made to route to target sites following paths embedded in the 2D DNA lattices (in contrast, prior DNA walkers traversed only linear DNA nanostructures). (b) The DNA walkers will be able process information embedded along its path and perform finite state operations on the sequence of information it encounters. We will also self-assemble for the first time fully addressable two dimensional DNA lattices, on which the programmable paths of the walkers will be defined. We will also extend the DNA walkers to nano-transport devices: that is, (a) to transport a variety of types (e.g., metallic particles and proteins) of nano-particles, (b) to pick up and unload nano-particles at specific sites on the DNA lattice, and (c) to cooperatively carry a DNA lattice as a load. These much improved DNA walkers will be of two types: (a) One type is an extension of previous autonomous walkers developed at Duke and is based on protein enzymes; (b) the other type is made purely of nucleic acids and does not use protein enzymes. In addition to the design and computer simulation of these improved DNA walkers, the proposed work includes a series of experimental demonstrations of isolated capabilities of DNA walkers as listed above, as well as experimental demonstrations of general operations such as lattice-wide transporting/processing of information and transporting of material. The proposed work is inherently cross-disciplinary and will impact multiple ?elds including chemistry, biochemistry, physics, computer science, and robotics, with potential long-term applications in nano-engineering and possibly in areas of biomedical interests. It will provide exciting and challenging interdisciplinary training opportunities for Duke graduate and undergraduate students. This project will provide a transition from the existing simple nano-effectors to programmable nano-robotics network system, yielding capabilities that have broad impact to nano-engineering. There are numerous feasible practical applications of our proposed autonomous programmable molecular transport network. For example, such a programmable nano-particle transport system might be used in the future for constructing complex assemblies of various nano-electronic devices attached to specified sites on the DNA lattice and for detecting/processing/broadcasting molecular signals.