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23rd international conference on dna computing and molecular programming, dna 2017

ISBN: (纸本)9783319667980

The proceedings contain 16 papers. The special focus in this conference is on dna computing and molecular programming. The topics include: Automated, constraint-based analysis of tethered dna nanostructures;dna-templated synthesis optimization;ruleset optimization on isomorphic oritatami systems;unknotted strand routings of triangulated meshes;the design space of strand displacement cascades with toehold-size clamps;a stochastic molecular scheme for an artificial cell to infer its environment from partial observations;complexities for high-temperature two-handed tile self-assembly;a dna neural network constructed from molecular variable gain amplifiers;a stochastic approach to shortcut bridging in programmable matter;a minimal requirement for self-assembly of lines in polylogarithmic time;robust detection in leak-prone population protocols;inferring parameters for an elementary step model of dna structure kinetics with locally context-dependent arrhenius rates;simplifying analyses of chemical reaction networks for approximate majority;chemical boltzmann machines;a general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities and thermodynamic binding networks.

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Novel Design of dna Constant-Signal Generator Towards an Experimental Feasibility 23

Novel Design of DNA Constant-Signal Generator Towards an Exp...

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23rd international conference on Control, Automation and Systems, ICCAS 2023

作者： Fujimura, Takeru Nakakuki, Takashi Kyushu Institute of Technology Department of Intelligent and Control Systems Fukuoka Japan

ISBN: (纸本)9788993215274

Dynamics dna nanotechnology is currently the most common method for designing molecular circuits, referred to as dna circuits, which can process complex information by utilizing dna strands as information molecules. However, dna circuits are highly retroactive, that is, they have low modularity, which is a significant limitation in rational circuit design in the field of dna computing. A common issue is the significant decrease in the input signal applied to the circuit, which causes serious errors in arithmetic circuits, where fluctuations in the input levels can result in incorrect outcomes. Currently, there is no dna signal generator that can produce a constant input. In this study, we developed a practical design for a constant-signal generator based on a dna strand displacement mechanism to address the issue of decreasing input signals caused by low modularity in dna circuits. Notably, the proposed constant-signal generator had low retroactivity and was therefore highly independent, enabling the maintenance of the desired performance even when dna circuits were connected as loads. © 2023 ICROS.

关键词： dna

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Novel Design of dna Constant-Signal Generator Towards an Experimental Feasibility

Novel Design of DNA Constant-Signal Generator Towards an Exp...

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international conference on Control, Automation and Systems ( ICCAS)

作者： Takeru Fujimura Takashi Nakakuki Department of Intelligent and Control Systems Kyushu Institute of Technology Fukuoka Japan

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Automated analysis of tethered dna nanostructures using constraint solving

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NATURAL computing 2018年第4期17卷 709-722页

作者： Lakin, Matthew R. Phillips, Andrew Univ New Mexico Dept Comp Sci Ctr Biomed Engn Albuquerque NM 87131 USA Microsoft Res 21 Stn Rd Cambridge CB1 2FB England

Implementing dna computing circuits using components tethered to a surface offers several advantages over using components that freely diffuse in bulk solution. However, automated computational modeling of tethered circuits is far more challenging than for solution-phase circuits, because molecular geometry must be taken into account when deciding whether two tethered species may interact. Here, we tackle this issue by translating a tethered molecular circuit into a constraint problem that encodes the possible physical configurations of the components, using a simple biophysical model. We use a satisfaction modulo theories solver to determine whether the constraint problem associated with a given structure is satisfiable, which corresponds to whether that structure is physically realizable given the constraints imposed by the tether geometry. We apply this technique to example structures from the literature, and discuss how this approach could be integrated with a reaction enumerator to enable fully automated analysis of tethered molecular computing systems. This paper is a significantly revised and extended version of a conference publication: Lakin and Phillips (in Brijder and Qian (eds) Proceedings of the 23rd international conference on dna computing and molecular programming. Lecture Notes in Computer Science, vol 10467, pp 1-16, 2017).

关键词： molecular computing Tethered dna nanostructures molecular geometry dna strand displacement

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Single-Stranded Architectures for computing 23rd

Single-Stranded Architectures for Computing

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23rd international conference on Developments in Language Theory (DLT)

作者： Seki, Shinnosuke Univ Electrocommun 1-5-1 Chofugaoka Chofu Tokyo 1828585 Japan Ecole Normale Super Lyon 46 Allee Italie F-69007 Lyon France

ISBN: (纸本)9783030248857;9783030248864

RNA is a chain of ribonucleotides of four kinds (denoted respectively by the letters A, C, G, U). While being synthesized sequentially from its template dna (transcription), it folds upon itself into intricate higher-dimensional structures in such a way that the free energy is minimized, that is, the more hydrogen bonds between ribonucletoides or larger entropy a structure has, the more likely it is chosen, and furthermore the minimization is done locally. This phenomenon is called cotranscriptional folding (CF). It has turned out to play significant roles in in-vivo computation throughout experiments and recently proven even programmable artificially so as to self-assemble a specific RNA rectangular tile structure in vitro. The next step is to program a computation onto dna in such a way that the computation can be "called" by cotranscriptional folding. In this novel paradigm of computation, what programmers could do is only twofold: designing a template dna and setting environmental parameters. Oritatami is an introductory "toy" model to this paradigm of computation. In this model, programmars are also allowed to employ an arbitrarily large finite alphabet Sigma as well as an arbitrarily complex rule set for binding over Sigma x Sigma. We shall present known architectures of computing in the oritatami model from a simple half-adder to Turing machine along with several programming techniques of use, with hope that they will inspire in-vivo architectures of CF-driven self-assemblable computers, which could be even heritable.

关键词： RNA

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Unknotted Strand Routings of Triangulated Meshes 1

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23rd international conference on dna computing and molecular programming (dna)

作者： Mohammed, Abdulmelik Hajij, Mustafa Aalto Univ Espoo Finland Univ S Florida Tampa FL USA

ISBN: (数字)9783319667997

ISBN: (纸本)9783319667997;9783319667980

In molecular self-assembly such as dna origami, a circular strand's topological routing determines the feasibility of a design to assemble to a target. In this regard, the Chinese-postman dna scaffold routings of Benson et al. (2015) only ensure the unknottedness of the scaffold strand for triangulated topological spheres. In this paper, we present a cubic-time 5/3-approximation algorithm to compute unknotted Chinese-postman scaffold routings on triangulated orientable surfaces of higher genus. Our algorithm guarantees every edge is routed at most twice, hence permitting low-packed designs suitable for physiological conditions.

关键词： dna origami Knot theory Graph theory Chinese postman problem

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dna-Templated Synthesis Optimization 1

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23rd international conference on dna computing and molecular programming (dna)

作者： Hansen, Bjarke N. Larsen, Kim S. Merkle, Daniel Mihalchuk, Alexei Univ Southern Denmark Dept Math & Comp Sci Odense Denmark

ISBN: (数字)9783319667997

ISBN: (纸本)9783319667997;9783319667980

In chemistry, synthesis is the process in which a target compound is produced in a step-wise manner from given base compounds. A recent, promising approach for carrying out these reactions is dna-templated synthesis, since, as opposed to more traditional methods, this approach leads to a much higher effective molarity and makes much desired one-pot synthesis possible. With this method, compounds are tagged with dna sequences and reactions can be controlled by bringing two compounds together via their tags. This leads to new cost optimization problems of minimizing the number of different tags or strands to be used under various conditions. We identify relevant optimization criteria, provide the first computational approach to automatically inferring dna-templated programs, and obtain optimal and near-optimal results.

关键词： dna sequences

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Automated, Constraint-Based Analysis of Tethered dna Nanostructures 1

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23rd international conference on dna computing and molecular programming (dna)

作者： Lakin, Matthew R. Phillips, Andrew Univ New Mexico Dept Comp Sci Albuquerque NM 87131 USA Univ New Mexico Ctr Biomed Engn Albuquerque NM 87131 USA Univ New Mexico Dept Chem & Biol Engn Albuquerque NM 87131 USA Microsoft Res 21 Stn Rd Cambridge CB1 2FB England

ISBN: (数字)9783319667997

ISBN: (纸本)9783319667997;9783319667980

Implementing dna computing circuits using components tethered to a surface offers several advantages over using components that freely diffuse in bulk solution. However, automated computational modeling of tethered circuits is far more challenging than for solutionphase circuits, because molecular geometry must be taken into account when deciding whether two tethered species may interact. Here, we tackle this issue by translating a tethered molecular circuit into a constraint problem that encodes the possible physical configurations of the components, using a simple biophysical model. We use a satisfaction modulo theories (SMT) solver to determine whether the constraint problem associated with a given structure is satisfiable, which corresponds to whether that structure is physically realizable given the constraints imposed by the tether geometry. We apply this technique to example structures from the literature, and discuss how this approach could be integrated with a reaction enumerator to enable fully automated analysis of tethered molecular computing systems.

关键词： Computation theory

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A dna Neural Network Constructed from molecular Variable Gain Amplifiers 1

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23rd international conference on dna computing and molecular programming (dna)

作者： Chen, Sherry Xi Seelig, Georg Univ Washington Seattle WA 98195 USA

ISBN: (数字)9783319667997

ISBN: (纸本)9783319667997;9783319667980

Biological nucleic acids have important roles as diagnostic markers for disease. The detection of just one molecular marker, such as a dna sequence carrying a single nucleotide variant (SNV), can sometimes be indicative of a disease state. However, a reliable diagnosis and treatment decision often requires interpreting a combination of markers via complex algorithms. Here, we describe a diagnostic technology based on dna strand displacement that combines single nucleotide specificity with the ability to interpret the information encoded in panels of single-stranded nucleic acids through a molecular neural network computation. Our system is constructed around a single building block-a catalytic amplifier with a competitive inhibitor or "sink." In previous work, we demonstrated that such a system can be used to reliably detect SNVs in single stranded nucleic acids. Here, we show that these same building blocks can be reconfigured to create an amplification system with adjustable gain alpha. That is, the concentration of an output signal produced is exactly alpha times larger than the concentration of input added initially, and the value of a can be adjusted experimentally. Finally, we demonstrate that variable gain amplification and mismatch discrimination elements can be combined into a two-input neural network classifier. Together, our results suggest a novel approach for engineering molecular classifier circuits with predictable behaviors.

关键词： dna strand displacement Linear classifier Variable gain amplifier Neural network microRNA Competitive inhibition

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Inferring Parameters for an Elementary Step Model of dna Structure Kinetics with Locally Context-Dependent Arrhenius Rates 1

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23rd international conference on dna computing and molecular programming (dna)

作者： Zolaktaf, Sedigheh Dannenberg, Frits Rudelis, Xander Condon, Anne Schaeffer, Joseph M. Schmidt, Mark Thachuk, Chris Winfree, Erik Univ British Columbia Vancouver BC Canada CALTECH Pasadena CA 91125 USA Autodesk Res San Francisco CA USA

ISBN: (数字)9783319667997

ISBN: (纸本)9783319667997;9783319667980

Models of nucleic acid thermal stability are calibrated to a wide range of experimental observations, and typically predict equilibrium probabilities of nucleic acid secondary structures with reasonable accuracy. By comparison, a similar calibration and evaluation of nucleic acid kinetic models to a broad range of measurements has not been attempted so far. We introduce an Arrhenius model of interacting nucleic acid kinetics that relates the activation energy of a state transition with the immediate local environment of the affected base pair. Our model can be used in stochastic simulations to estimate kinetic properties and is consistent with existing thermodynamic models. We infer parameters for our model using an ensemble Markov chain Monte Carlo (MCMC) approach on a training dataset with 320 kinetic measurements of hairpin closing and opening, helix association and dissociation, bubble closing and toehold-mediated strand exchange. Our new model surpasses the performance of the previously established Metropolis model both on the training set and on a testing set of size 56 composed of toehold-mediated 3-way strand displacement with mismatches and hairpin opening and closing rates: reaction rates are predicted to within a factor of three for 93.4% and 78.5% of reactions for the training and testing sets, respectively.

关键词： Nucleic acids

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