A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures
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Erik Winfree | Stefan Badelt | Casey Grun | Karthik V. Sarma | Brian Wolfe | Seung Woo Shin | Brian R. Wolfe | E. Winfree | S. Shin | Stefan Badelt | C. Grun | Karthik V. Sarma | Casey Grun
[1] Eric Jones,et al. SciPy: Open Source Scientific Tools for Python , 2001 .
[2] Miran Liber,et al. Detailed study of DNA hairpin dynamics using single-molecule fluorescence assisted by DNA origami. , 2013, The journal of physical chemistry. B.
[3] G. Seelig,et al. Enzyme-Free Nucleic Acid Logic Circuits , 2022 .
[4] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[5] Peng Yin,et al. Optimizing the specificity of nucleic acid hybridization. , 2012, Nature chemistry.
[6] Matthew R. Lakin,et al. Bioinformatics Applications Note Systems Biology Visual Dsd: a Design and Analysis Tool for Dna Strand Displacement Systems , 2022 .
[7] Masami Hagiya,et al. DNA computation simulator based on abstract bases , 2001, Soft Comput..
[8] David H Mathews,et al. RNA Secondary Structure Analysis Using RNAstructure , 2006, Current protocols in bioinformatics.
[9] J. Wetmur. Hybridization and renaturation kinetics of nucleic acids. , 1976, Annual review of biophysics and bioengineering.
[10] N. Pierce,et al. A synthetic DNA walker for molecular transport. , 2004, Journal of the American Chemical Society.
[11] Luca Cardelli,et al. Abstractions for DNA circuit design , 2011, Journal of The Royal Society Interface.
[12] G. Seelig,et al. Dynamic DNA nanotechnology using strand-displacement reactions. , 2011, Nature chemistry.
[13] Luca Cardelli,et al. Two-domain DNA strand displacement , 2010, Mathematical Structures in Computer Science.
[14] Conrad Steenberg,et al. NUPACK: Analysis and design of nucleic acid systems , 2011, J. Comput. Chem..
[15] David H Mathews,et al. RNA pseudoknots: folding and finding , 2010, F1000 biology reports.
[16] P. Hsieh,et al. The kinetics of spontaneous DNA branch migration. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[17] E. Andersen. Prediction and design of DNA and RNA structures. , 2010, New biotechnology.
[18] Hamidreza Chitsaz,et al. A partition function algorithm for interacting nucleic acid strands , 2009, Bioinform..
[19] W. Hughes,et al. Multi-Arm Junctions for Dynamic DNA Nanotechnology. , 2017, Journal of the American Chemical Society.
[20] Grégoire Altan-Bonnet,et al. Bubble dynamics in double-stranded DNA. , 2003, Physical review letters.
[21] D. Y. Zhang,et al. Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.
[22] Hagiya Masami,et al. Abstraction of DNA Graph Structures for Efficient Enumeration and Simulation , 2011 .
[23] Matthew R. Lakin,et al. Modelling, Simulating and Verifying Turing-Powerful Strand Displacement Systems , 2011, DNA.
[24] G. Seelig,et al. DNA as a universal substrate for chemical kinetics , 2010, Proceedings of the National Academy of Sciences.
[25] Erik Winfree,et al. Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands , 2015, DNA.
[26] Jonathan Bath,et al. Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. , 2011, Journal of the American Chemical Society.
[27] D. Porschke. A direct measurement of the unzippering rate of a nucleic acid double helix. , 1974 .
[28] Vincent Danos,et al. Internal coarse-graining of molecular systems , 2009, Proceedings of the National Academy of Sciences.
[29] Jehoshua Bruck,et al. Programmability of Chemical Reaction Networks , 2009, Algorithmic Bioprocesses.
[30] N. Seeman,et al. Operation of a DNA Robot Arm Inserted into a 2D DNA Crystalline Substrate , 2006, Science.
[31] J. SantaLucia,et al. The thermodynamics of DNA structural motifs. , 2004, Annual review of biophysics and biomolecular structure.
[32] Niles A. Pierce,et al. An algorithm for computing nucleic acid base‐pairing probabilities including pseudoknots , 2004, J. Comput. Chem..
[33] F. Simmel,et al. Principles and Applications of Nucleic Acid Strand Displacement Reactions. , 2019, Chemical reviews.
[34] D. Turner,et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[35] Erik Winfree,et al. Verifying Chemical Reaction Network Implementations: A Bisimulation Approach , 2016, DNA.
[36] D. Turner,et al. RNA structure prediction. , 1988, Annual review of biophysics and biophysical chemistry.
[37] P. Schuster,et al. RNA folding at elementary step resolution. , 1999, RNA.
[38] N. Destainville,et al. Physics of base-pairing dynamics in DNA , 2015, 1510.05574.
[39] E. Siggia,et al. Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[40] A. Ansari,et al. A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics. , 2012, Biophysical journal.
[41] Hieu Bui,et al. Modeling DNA Nanodevices Using Graph Rewrite Systems , 2017 .
[42] K. Hall,et al. Millisecond time-scale folding and unfolding of DNA hairpins using rapid-mixing stopped-flow kinetics. , 2012, Journal of the American Chemical Society.
[43] P. Rothemund. Folding DNA to create nanoscale shapes and patterns , 2006, Nature.
[44] James R Faeder,et al. Rule-based modeling of biochemical systems with BioNetGen. , 2009, Methods in molecular biology.
[45] Robert E. Tarjan,et al. Depth-First Search and Linear Graph Algorithms , 1972, SIAM J. Comput..
[46] J. Doye,et al. DNA hybridization kinetics: zippering, internal displacement and sequence dependence , 2013, Nucleic acids research.
[47] Erik Winfree,et al. Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems , 2018, Journal of the Royal Society Interface.
[48] Lulu Qian,et al. Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks , 2018, Nature.
[49] Erik Winfree,et al. Thermodynamic Analysis of Interacting Nucleic Acid Strands , 2007, SIAM Rev..
[50] J. Wetmur. DNA probes: applications of the principles of nucleic acid hybridization. , 1991, Critical reviews in biochemistry and molecular biology.
[51] Masami Hagiya,et al. Abstraction of Graph-Based Models of Bio-molecular Reaction Systems for Efficient Simulation , 2012, CMSB.
[52] Daniel Merkle,et al. A Software Package for Chemically Inspired Graph Transformation , 2016, ICGT.
[53] D. Y. Zhang,et al. Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.
[54] Erik Winfree,et al. Leakless DNA Strand Displacement Systems , 2015, DNA.
[55] Erik Winfree,et al. A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities , 2017, DNA.
[56] David Yu Zhang,et al. Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions , 2010, DNA.
[57] N. Seeman. Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.
[58] E Rivas,et al. A dynamic programming algorithm for RNA structure prediction including pseudoknots. , 1998, Journal of molecular biology.
[59] P. Yin,et al. Complex shapes self-assembled from single-stranded DNA tiles , 2012, Nature.
[60] N. Gates,et al. Kinetics of Renaturation of DNA , 2003 .
[61] P. Stadler,et al. RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties , 1999, Bulletin of mathematical biology.
[62] A Libchaber,et al. Kinetics of conformational fluctuations in DNA hairpin-loops. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[63] N. Seeman,et al. A precisely controlled DNA biped walking device , 2004 .
[64] N. Seeman,et al. Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.
[65] E. Winfree,et al. Synthetic in vitro transcriptional oscillators , 2011, Molecular systems biology.
[66] Niles A Pierce,et al. Sequence Design for a Test Tube of Interacting Nucleic Acid Strands. , 2015, ACS synthetic biology.
[67] Xi Chen,et al. Shaping up nucleic acid computation. , 2010, Current opinion in biotechnology.
[68] Lorenzo Rovigatti,et al. Coarse-graining DNA for simulations of DNA nanotechnology. , 2013, Physical chemistry chemical physics : PCCP.
[69] D. W. Staple,et al. Open access, freely available online Primer Pseudoknots: RNA Structures with Diverse Functions , 2022 .
[70] E. Winfree,et al. Algorithmic Self-Assembly of DNA Sierpinski Triangles , 2004, PLoS biology.
[71] Le A. Trinh,et al. Programmable in situ amplification for multiplexed imaging of mRNA expression , 2010, Nature Biotechnology.
[72] Erik Winfree,et al. Enzyme-free nucleic acid dynamical systems , 2017, Science.
[73] Richard A. Muscat,et al. A programmable molecular robot. , 2011, Nano letters.
[74] Robert M. Dirks,et al. Triggered amplification by hybridization chain reaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[75] Nicholas J Porubsky,et al. Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering. , 2017, Journal of the American Chemical Society.
[76] L. Stols,et al. Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution. , 1993, Biochemistry.
[77] Vincent Danos,et al. Rule-Based Modelling of Cellular Signalling , 2007, CONCUR.
[78] Erik Winfree,et al. Effective design principles for leakless strand displacement systems , 2018, Proceedings of the National Academy of Sciences.
[79] Lulu Qian,et al. Efficient Turing-Universal Computation with DNA Polymers , 2010, DNA.
[80] Mark W. Schmidt,et al. Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates , 2017, DNA.
[81] Luca Cardelli,et al. A programming language for composable DNA circuits , 2009, Journal of The Royal Society Interface.
[82] David H. Mathews,et al. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure , 2009, Nucleic Acids Res..
[83] Daniel T Gillespie,et al. Stochastic simulation of chemical kinetics. , 2007, Annual review of physical chemistry.
[84] Michael S. Samoilov,et al. Automated Abstraction Methodology for Genetic Regulatory Networks , 2006, Trans. Comp. Sys. Biology.
[85] A. Turberfield,et al. DNA fuel for free-running nanomachines. , 2003, Physical review letters.
[86] Matthew R. Lakin,et al. A Logic Programming Language for Computational Nucleic Acid Devices. , 2018, ACS synthetic biology.
[87] M. Guéron,et al. Studies of base pair kinetics by NMR measurement of proton exchange. , 1995, Methods in enzymology.
[88] Justin Werfel,et al. DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology , 2015, Journal of The Royal Society Interface.
[89] Robert M. Dirks,et al. An autonomous polymerization motor powered by DNA hybridization , 2007, Nature Nanotechnology.
[90] Matthew R. Lakin,et al. A strand graph semantics for DNA-based computation , 2016, Theor. Comput. Sci..
[91] D. Crothers,et al. THE KINETICS OF DNA DENATURATION. , 1964, Journal of molecular biology.
[92] Friedrich C Simmel,et al. Nucleic acid based molecular devices. , 2011, Angewandte Chemie.
[93] Brian Munsky,et al. Reduction and solution of the chemical master equation using time scale separation and finite state projection. , 2006, The Journal of chemical physics.
[94] Joachim Niehren,et al. Structural Simplification of Chemical Reaction Networks Preserving Deterministic Semantics , 2015, CMSB.
[95] Christian M. Reidys,et al. Topology and prediction of RNA pseudoknots , 2011, Bioinform..
[96] Erik Winfree,et al. Robustness and modularity properties of a non-covalent DNA catalytic reaction , 2010, Nucleic acids research.
[97] P J Goss,et al. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[98] Lulu Qian,et al. Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .
[99] T. Pollard,et al. Annual review of biophysics and biophysical chemistry , 1985 .
[100] Ruojie Sha,et al. A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.
[101] S. Woodson,et al. Loop dependence of the stability and dynamics of nucleic acid hairpins , 2007, Nucleic acids research.
[102] Luca Cardelli,et al. Programmable chemical controllers made from DNA. , 2013, Nature nanotechnology.
[103] Nadine L. Dabby,et al. Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs, and Experimental Study , 2013 .
[104] N. Seeman. Nanomaterials based on DNA. , 2010, Annual review of biochemistry.
[105] Matthew R. Lakin,et al. Modular Verification of DNA Strand Displacement Networks via Serializability Analysis , 2013, DNA.
[106] A. Turberfield,et al. A DNA-fuelled molecular machine made of DNA , 2022 .
[107] David Yu Zhang,et al. Cooperative hybridization of oligonucleotides. , 2011, Journal of the American Chemical Society.
[108] Joseph M. Schaeffer,et al. On the biophysics and kinetics of toehold-mediated DNA strand displacement , 2013, Nucleic acids research.
[109] Peter F. Stadler,et al. ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.
[110] Jehoshua Bruck,et al. Neural network computation with DNA strand displacement cascades , 2011, Nature.
[111] Harry M. T. Choi,et al. Programming biomolecular self-assembly pathways , 2008, Nature.
[112] Lulu Qian,et al. Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components , 2017, Nature Communications.
[113] P. Hsieh,et al. Formation of a single base mismatch impedes spontaneous DNA branch migration. , 1993, Journal of molecular biology.
[114] Xi Chen,et al. Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits. , 2012, Journal of the American Chemical Society.
[115] Erik Winfree,et al. Verifying Chemical Reaction Network Implementations: A Pathway Decomposition Approach , 2014, Theor. Comput. Sci..