Toward reliable algorithmic self-assembly of DNA tiles: A fixed-width cellular automaton pattern

Bottom-up fabrication of nanoscale structures relies on chemical processes to direct self-assembly. The complexity, precision, and yield achievable by a one-pot reaction are limited by our ability to encode assembly instructions into the molecules themselves. Nucleic acids provide a platform for investigating these issues, as molecular structure and intramolecular interactions can encode growth rules. Here, we use DNA tiles and DNA origami to grow crystals containing a cellular automaton pattern. In a one-pot annealing reaction, 250 DNA strands first assemble into a set of 10 free tile types and a seed structure, then the free tiles grow algorithmically from the seed according to the automaton rules. In our experiments, crystals grew to ~300 nm long, containing ~300 tiles with an initial assembly error rate of ~1.4% per tile. This work provides evidence that programmable molecular self-assembly may be sufficient to create a wide range of complex objects in one-pot reactions

Status Report of Neutral Kaon photo-production study using Neutral Kaon Spectrometer 2 (NKS2) at LNS-Tohoku(I. Nuclear Physics)

The approach described in this paper uses an array of Field Programmable Gate Array (FPGA) devices to implement a fault tolerant hardware system that can be compared to the running of fault tolerant software on a traditional processor. Fault tolerance is achieved is achieved by using FPGA with on the fly partial programmability feature. Major considerations while mapping to the FPGA includes the size of the area to be mapped and communication issues related to their communication. Area size selection is compared to the page size selection in Operating System Design. Communication issues between modules are compared to the software engineering paradigms dealing with module coupling, fan-in, fan-out and cohesiveness. Finally, the overhead associated with the downloading of the reconfiguration files is discussed

Error suppression mechanisms for DNA tile self-assembly and their simulation

Algorithmic self-assembly using DNA-based molecular tiles has been demonstrated to implement molecular computation. When several different types of DNA tile self-assemble, they can form large two-dimensional algorithmic patterns. Prior analysis predicted that the error rates of tile assembly can be reduced by optimizing physical parameters such as tile concentrations and temperature. However, in exchange, the growth speed is also very low. To improve the tradeoff between error rate and growth speed, we propose two novel error suppression mechanisms: the Protected Tile Mechanism (PTM) and the Layered Tile Mechanism (LTM). These utilize DNA protecting molecules to form kinetic barriers against spurious assembly. In order to analyze the performance of these two mechanisms, we introduce the hybridization state Tile Assembly Model (hsTAM), which evaluates intra-tile state changes as well as assembly state changes. Simulations using hsTAM suggest that the PTM and LTM improve the optimal tradeoff between error rate ε and growth speed r, from r ≈ βε^(2.0) (for the conventional mechanism) to r ≈ βε^(1.4) and r ≈ βε^(0.7), respectively

Comparison of in vitro characteristics of a monomeric, dimeric and trimeric fibronectin-derived linear

Multivalent interactions are frequently used to enhance ligand-receptor binding affinity. In this study a mono-, di- and trimeric AVTGRGDSY peptide derived from fibronectin were compared concerning the integrin receptor binding affinity and/or specificity. Methods: AVTGRGDSY monomer, dimer and trimer were synthesized, labeled with 125I or Cy5.5. Using human embryonic kidney cells HEK293 (naturally alphaV-positive and beta3-negative), HEK293(beta1) (beta1-transfected and alphaVbeta3-negative), HEK293(beta3)( beta3-transfected and strongly alphaVbeta3-positive), and human glioblastoma cells U87MG (naturally alphaVbeta3-positive),cell-binding assay, competitive inhibition assay, cell adhesion assay and confocal laser scanning microscopic study were performed to determine the bioactivities of these peptides. Results: The monomeric AVTGRGDSY showed specific binding to both HEK293(beta1) and HEK293(beta3) cells. Multimerization resulted in no change with HEK293 cells, diminished binding for HEK293(beta1) cells, but substantially enhanced binding for alphaVbeta3-positive HEK293(beta3) and U87MG cells in the presence of Mn2+. Moreover, the multimeric AVTGRGDSY peptides were found to be nearly comparable with th alphaVbeta3-specific cyclo(RGDfV) peptide in specificity and affinity for targeting alphaVbeta3 integrin. Conclusion: The multimeric AVTGRGDSY peptide might be an efficient alphaVbeta3-targeting molecule. The present study would be useful for better understanding of the molecular basis of the interaction between RGD ligands and integrin receptors.World Molecular Imaging Congres