Intelligent nanomechanical devices that operate in an autonomous fashion are of great theoretical and practical interest. Recent successes in building large scale DNA nanostructures, 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 a DNA mechanical device that is capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical designs and a prototype experimental construction of autonomous unidirectional DNA walking devices that move along linear tracks, we present in this paper the design of a nanomechanical DNA device that autonomously mimics the operation of a 2-state 5color universal Turing machine. Our autonomous nanomechanical device, which we call an Autonomous DNA Turing Machine, is thus capable of universal computation and hence complex translational motion which we define as universal translational motion.

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, nanoelectronics, nano-diagnostics/therapeutics, and nanocomputing. 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.

ABSTRACT Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. They are found as intermediates in meiosis and they have been used extensively in structural DNA nanotechnology for the construction of one-dimensional and two-dimensional arrays and in a DNA nanomechanical device. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half-turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, facilitating their characterization in a ligation cyclization assay. Hence, we have estimated the flexibility of antiparallel DNA double crossover molecules by means of ligation-closure experiments. We are able to show that these molecules are approximately twice as rigid as linear duplex DNA.

Polymerases are a family of enzymes responsible for copying or replication of nucleic acids (DNA or RNA) templates and hence sustenance of life processes. In this paper, we present a method to exploit a strand-displacing polymerase φ29 as a driving force for nanoscale transportation devices. The principle idea behind the device is strong strand displacement ability of φ29, which can displace any DNA strand from its template while extending a primer hybridized to the template. This capability of φ29 is used to power the movement of a target nanostructure on a DNA track. The major advantage of using a polymerase driven nanotransportation device as compared to other existing nanorobotical devices is its speed. φ29 polymerase can travel at the rate of 2000 nucleotides per minute [1] at room temperature, which translates to approximately 680 nanometers per minute on a nanostructure. We also demonstrate transportation of a DNA cargo on a

A major challenge in nanoscience is the design of synthetic molecular devices that run autonomously and are programmable. DNA-based synthetic molecular devices have the advantage of being relatively simple to design and engineer, due to the predictable secondary structure of DNA nanostructures and the well-established biochemistry used to manipulate DNA nanostructures. We present the design of a class of DNAzyme based molecular devices that are autonomous, programmable, and further require no protein enzymes. The basic principle involved is inspired by a simple but ingenious molecular device due to Mao et al [25]. Our DNAzyme based designs include (1) a finite state automata device, DNAzyme FSA that executes finite state transitions using DNAzymes, (2) extensions to it including probabilistic automata and non-deterministic automata, (3) its application as a DNAzyme router for programmable routing of nanostructures on a 2D DNA addressable lattice, and (4) a medical-related application, DNAzyme doctor that provide transduction of nucleic acid expression: it can be programmed to respond to the underexpression or overexpression of various strands of RNA, with a response by release of an RNA.

Abstract: A practical theoretical framework is presented for designing and classifying minimally strained nucleic acid nanotubes. The structures are based on the double crossover motif where each double helical domain is connected to each of its neighbors via two or more Holliday junction-like reciprocal exchanges, such that each domain is parallel to the main tube axis. Modeling is based on a 5-parameter characterization of the segmented double-helical structure. Once the constraint equations have been derived, the primary design problem for a minimally strained N-domain structure is reduced to solving 3 simultaneous equations in 2N+2 variables. Symmetry analysis and tube merging then allow for the design of a wide variety of tubes, which can be tailored to satisfy requirements such as specific inner-and-outer radii, or multiple lobed structures. The general form of the equations allows similar techniques to be applied to various nucleic acid helices: B-DNA, A-DNA, RNA, DNA-PNA, or others. Possible applications for such tubes include nano-scale scaffolding as well as custom shaped enclosures for other nanoobjects.

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DNA-based nanotechnology has been attractive as a novel assembly method for fabricating nanostructures for the last two decades. Artificially designed, self-assembled DNA nanostructures have been reported with various geometrical structures and functionalities: one- and two-dimensional periodically patterned structures, threedimensional polyhedra, nanomechanical devices, molecular computers, and organization of other functionalized molecules. This thesis describes self-assembled DNA nanostructures and DNA-templated metallic nanowires. One- and two- dimensional periodically patterned superstructures, such as filaments, lattices, nanoribbons, nanotracks, and nanogrids, utilizing newly conceived two distinct DNA motifs- three helix bundles, and the cross-tiles as well as synthetic double-stranded DNA molecules-will be discussed with unique design schemes and characteristics. DNA complexes have been visualized by high-resolution tapping mode atomic force microscopy under buffer. Their dimensions are shown to be in excellent agreement with designed structures. We have also presented fabrication of size-controllable, fully addressable, and precisely

The construction of complex systems at the 1- 100 nanometer (1 nanometer = ¡£¢¥¤§ ¦ meter) scale is a key challenge in current nanoscience. This challenge can be most effectively ad-dressed by the “bottom-up ” nano-construction methodology based on self-assembly, a pro-cess in which substructures autonomously associate with each other to form superstructures driven by the selective affinity of the substructures. DNA, with its immense information encoding capacity and well defined Watson-Crick complementarity, has recently emerged as an excellent material for constructing self-assembled nano-structures. In this disserta-tion, we study four closely related aspects of DNA based self-assembly and nano-devices: complexity of self-assembly, fault-tolerant self-assembly, DNA robotics devices, and DNA computing devices. Complexity of self-assembly. We establish a framework that models assemblies result-ing from the cooperative effects of repulsion and attraction forces in a general setting of