Evolving Gene Regulatory Networks with Mobile DNA Mechanisms

This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming increasingly clear. This paper shows how dynamically controlling network node connectivity and function via transposon-inspired mechanisms can be selected for in computational intelligence tasks to give improved performance. The designs of dynamical networks intended for implementation within the slime mould Physarum polycephalum and for the distributed control of a smart surface are considered.Comment: 7 pages, 8 figures. arXiv admin note: substantial text overlap with arXiv:1303.722

DNA multi-bit non-volatile memory and bit-shifting operations using addressable electrode arrays and electric field-induced hybridization.

DNA has been employed to either store digital information or to perform parallel molecular computing. Relatively unexplored is the ability to combine DNA-based memory and logical operations in a single platform. Here, we show a DNA tri-level cell non-volatile memory system capable of parallel random-access writing of memory and bit shifting operations. A microchip with an array of individually addressable electrodes was employed to enable random access of the memory cells using electric fields. Three segments on a DNA template molecule were used to encode three data bits. Rapid writing of data bits was enabled by electric field-induced hybridization of fluorescently labeled complementary probes and the data bits were read by fluorescence imaging. We demonstrated the rapid parallel writing and reading of 8 (23) combinations of 3-bit memory data and bit shifting operations by electric field-induced strand displacement. Our system may find potential applications in DNA-based memory and computations

Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes

This paper extends the study and prototyping of unusual DNA motifs, unknown in nature, but founded on principles derived from biological structures. Artificially designed DNA complexes show promise as building blocks for the construction of useful nanoscale structures, devices, and computers. The DNA triple crossover (TX) complex described here extends the set of experimentally characterized building blocks. It consists of four oligonucleotides hybridized to form three double-stranded DNA helices lying in a plane and linked by strand exchange at four immobile crossover points. The topology selected for this TX molecule allows for the presence of reporter strands along the molecular diagonal that can be used to relate the inputs and outputs of DNA-based computation. Nucleotide sequence design for the synthetic strands was assisted by the application of algorithms that minimize possible alternative base-pairing structures. Synthetic oligonucleotides were purified, stoichiometric mixtures were annealed by slow cooling, and the resulting DNA structures were analyzed by nondenaturing gel electrophoresis and heat-induced unfolding. Ferguson analysis and hydroxyl radical autofootprinting provide strong evidence for the assembly of the strands to the target TX structure. Ligation of reporter strands has been demonstrated with this motif, as well as the self-assembly of hydrogen-bonded two-dimensional crystals in two different arrangements. Future applications of TX units include the construction of larger structures from multiple TX units, and DNA-based computation. In addition to the presence of reporter strands, potential advantages of TX units over other DNA structures include space for gaps in molecular arrays, larger spatial displacements in nanodevices, and the incorporation of well-structured out-of-plane components in two-dimensional arrays

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