Experimental Progress in Computation by Self-Assembly of DNA Tilings

Approaches to DNA-based computing by self-assembly require the use of D. T A nanostructures, called tiles, that have efficient chemistries, expressive computational power: and convenient input and output (I/O) mechanisms. We have designed two new classes of DNA tiles: TAO and TAE, both of which contain three double-helices linked by strand exchange. Structural analysis of a TAO molecule has shown that the molecule assembles efficiently from its four component strands. Here we demonstrate a novel method for I/O whereby multiple tiles assemble around a single-stranded (input) scaffold strand. Computation by tiling theoretically results in the formation of structures that contain single-stranded (output) reported strands, which can then be isolated for subsequent steps of computation if necessary. We illustrate the advantages of TAO and TAE designs by detailing two examples of massively parallel arithmetic: construction of complete XOR and addition tables by linear assemblies of DNA tiles. The three helix structures provide flexibility for topological routing of strands in the computation: allowing the implementation of string tile models

Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments

Biology makes things far smaller and more complex than anything produced by human engineering. The biotechnology revolution has for the first time given us the tools necessary to consider engineering on the molecular level. Research in DNA computation, launched by Len Adleman, has opened the door for experimental study of programmable biochemical reactions. Here we focus on a single biochemical mechanism, the self-assembly of DNA structures, that is theoretically sufficient for Turing-universal computation. The theory combines Hao Wang?s purely mathematical Tiling Problem with the branched DNA constructions of Ned Seeman. In the context of mathematical logic, Wang showed how jigsaw-shaped tiles can be designed to simulate the operation of any Turing Machine. For a biochemical implementation, we will need molecular Wang tiles. DNA molecular structures and intermolecular interactions are particularly amenable to design and are sufficient for the creation of complex molecular objects. The structure of individual molecules can be designed by maximizing desired and minimizing undesired Watson-Crick complementarity. Intermolecular interactions are programmed by the design of sticky ends that determine which molecules associate, and how. The theory has been demonstrated experimentally using a system of synthetic DNA double-crossover molecules that self-assemble into two-dimensional crystals that have been visualized by atomic force microscopy. This experimental system provides an excellent platform for exploring the relationship between computation and molecular self-assembly, and thus represents a first step toward the ability to program molecular reactions and molecular structures

DNA Computing by Self-Assembly

Information and algorithms appear to be central to biological organization and processes, from the storage and reproduction of genetic information to the control of developmental processes to the sophisticated computations performed by the nervous system. Much as human technology uses electronic microprocessors to control electromechanical devices, biological organisms use biochemical circuits to control molecular and chemical events. The engineering and programming of biochemical circuits, in vivo and in vitro, would transform industries that use chemical and nanostructured materials. Although the construction of biochemical circuits has been explored theoretically since the birth of molecular biology, our practical experience with the capabilities and possible programming of biochemical algorithms is still very young

Two computational primitives for algorithmic self-assembly: Copying and counting

Copying and counting are useful primitive operations for computation and construction. We have made DNA crystals that copy and crystals that count as they grow. For counting, 16 oligonucleotides assemble into four DNA Wang tiles that subsequently crystallize on a polymeric nucleating scaffold strand, arranging themselves in a binary counting pattern that could serve as a template for a molecular electronic demultiplexing circuit. Although the yield of counting crystals is low, and per-tile error rates in such crystals is roughly 10%, this work demonstrates the potential of algorithmic self-assembly to create complex nanoscale patterns of technological interest. A subset of the tiles for counting form information-bearing DNA tubes that copy bit strings from layer to layer along their length

Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal

We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided their patch interactions are chosen in an appropriate way. Such patchy particles can be thought of as a coarse-grained representation of DNA multi-arm `star' motifs, which can be chosen to bond with one another very specifically by tuning the DNA sequences of the protruding arms. We explore several possible design strategies and conclude that DNA star tiles that are designed to interact with one another in a specific but not overly constrained way could potentially be used to construct soft quasicrystals in experiment. We verify that such star tiles can form stable dodecagonal motifs using oxDNA, a realistic coarse-grained model of DNA

Review on DNA Cryptography

Cryptography is the science that secures data and communication over the network by applying mathematics and logic to design strong encryption methods. In the modern era of e-business and e-commerce the protection of confidentiality, integrity and availability (CIA triad) of stored information as well as of transmitted data is very crucial. DNA molecules, having the capacity to store, process and transmit information, inspires the idea of DNA cryptography. This combination of the chemical characteristics of biological DNA sequences and classical cryptography ensures the non-vulnerable transmission of data. In this paper we have reviewed the present state of art of DNA cryptography.Comment: 31 pages, 12 figures, 6 table