Algorithmic Self-Assembly of DNA

Summary form only given. Nucleic acids have proven to be remarkably versatile as an engineering material for chemical tasks including the storage of information, catalyzing reactions creating and breaking bonds, mechanical manipulation using molecular motors, and constructing supramolecular structures. This talk will focus particularly on molecular self-assembly, giving examples of engineered DNA "tiles" that crystallize into two-dimensional sheets, one-dimensional tubes and ribbons, and information-guided patterns such as a Sierpinski triangle and a binary counter. A theme is how cooperative binding can be used to control nucleation and direct selective tile attachment. Such "algorithmic" self-assembly may provide a bottom-up fabrication method for creating complex, well-defined supramolecular structures that can be used as scaffolds or templates for applications such as arranging molecular electronic components into active circuits

[1]  Robert L. Berger The undecidability of the domino problem , 1966 .

[2]  Seymour Ginsburg,et al.  The mathematical theory of context free languages , 1966 .

[3]  Alvy Ray Smith,et al.  Simple Computation-Universal Cellular Spaces , 1971, JACM.

[4]  R. Robinson Undecidability and nonperiodicity for tilings of the plane , 1971 .

[5]  Charles H. Bennett,et al.  Logical reversibility of computation , 1973 .

[6]  Karl J. Smith Pascal's Triangle. , 1973 .

[7]  A. C. Chang,et al.  Construction of biologically functional bacterial plasmids in vitro. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Donald E. Knuth,et al.  The Art of Computer Programming: Volume 3: Sorting and Searching , 1998 .

[9]  J. Hopfield Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[10]  William P. Hanf,et al.  Nonrecursive tilings of the plane. I , 1974, Journal of Symbolic Logic.

[11]  Dale Myers,et al.  Nonrecursive tilings of the plane. II , 1974, Journal of Symbolic Logic.

[12]  M. V. Wilkes,et al.  The Art of Computer Programming, Volume 3, Sorting and Searching , 1974 .

[13]  M. Gefter,et al.  DNA Replication , 2019, Advances in Experimental Medicine and Biology.

[14]  Y. Pomeau,et al.  Molecular dynamics of a classical lattice gas: Transport properties and time correlation functions , 1976 .

[15]  J. Wang,et al.  Helical repeat of DNA in solution. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[16]  A. Klug,et al.  Helical periodicity of DNA determined by enzyme digestion , 1980, Nature.

[17]  Zvi Kam,et al.  Crystallization Processes of Biological Macromolecules , 1980 .

[18]  Self-Assembly and Nucleation of a Two-Dimensional Array of Protein Subunits , 1980 .

[19]  C. Cantor,et al.  Biophysical chemistry. Part III, The behavior of biologicalmacromolecules , 1980 .

[20]  R. A. Cox Biophysical Chemistry Part III: The Behavior of Biological Macromolecules , 1981 .

[21]  N. Seeman Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[22]  J J Hopfield,et al.  Neural networks and physical systems with emergent collective computational abilities. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Charles H. Bennett,et al.  The thermodynamics of computation—a review , 1982 .

[24]  S. Wolfram Geometry of Binomial Coefficients , 1984 .

[25]  N. Margolus Physics-like models of computation☆ , 1984 .

[26]  R C Haddon,et al.  The molecular electronic device and the biochip computer: present status. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[27]  M. Caruthers,et al.  Gene synthesis machines: DNA chemistry and its uses. , 1985, Science.

[28]  N C Seeman,et al.  Three-arm nucleic acid junctions are flexible. , 1986, Nucleic acids research.

[29]  D. A. Barrington BOUNDED WIDTH BRANCHING PROGRAMS , 1986 .

[30]  Gerber,et al.  Atomic Force Microscope , 2020, Definitions.

[31]  Tommaso Toffoli,et al.  Cellular automata machines - a new environment for modeling , 1987, MIT Press series in scientific computation.

[32]  Pavel Pudlák The hierarchy of Boolean circuits , 1987 .

[33]  Ingo Wegener,et al.  The complexity of Boolean functions , 1987 .

[34]  Tommaso Toffoli,et al.  Cellular Automata Machines , 1987, Complex Syst..

[35]  P J Steinhardt,et al.  The physics of quasicrystals , 1987 .

[36]  B H Robinson,et al.  The design of a biochip: a self-assembling molecular-scale memory device. , 1987, Protein engineering.

[37]  Péter Gács,et al.  A Simple Three-Dimensional Real-Time Reliable Cellular Array , 1988, J. Comput. Syst. Sci..

[38]  N. Seeman,et al.  The ligation and flexibility of four‐arm DNA junctions , 1988, Biopolymers.

[39]  Richard J. Lipton,et al.  Subquadratic simulations of circuits by branching programs , 1989, 30th Annual Symposium on Foundations of Computer Science.

[40]  Christoph Meinel,et al.  Modified Branching Programs and Their Computational Power , 1989, Lecture Notes in Computer Science.

[41]  R. S. Quartin,et al.  Effect of ionic strength on the hybridization of oligodeoxynucleotides with reduced charge due to methylphosphonate linkages to unmodified oligodeoxynucleotides containing the complementary sequence. , 1989, Biochemistry.

[42]  Vojtech Rödl,et al.  Lower Bounds to the Complexity of Symmetric Boolean Functions , 1990, Theor. Comput. Sci..

[43]  G. C. Shephard,et al.  Tilings and Patterns , 1990 .

[44]  Mats G. Nordahl,et al.  Universal Computation in Simple One-Dimensional Cellular Automata , 1990, Complex Syst..

[45]  N. Seeman De novo design of sequences for nucleic acid structural engineering. , 1990, Journal of biomolecular structure & dynamics.

[46]  Ravi B. Boppana,et al.  The Complexity of Finite Functions , 1991, Handbook of Theoretical Computer Science, Volume A: Algorithms and Complexity.

[47]  J. Van Leeuwen,et al.  Handbook of theoretical computer science - Part A: Algorithms and complexity; Part B: Formal models and semantics , 1990 .

[48]  Hao Wang Dominoes and the Aea Case of the Decision Problem , 1990 .

[49]  Alexander A. Razborov,et al.  Lower Bounds for Deterministic and Nondeterministic Branching Programs , 1991, FCT.

[50]  N. Seeman,et al.  Synthesis from DNA of a molecule with the connectivity of a cube , 1991, Nature.

[51]  J. Wetmur DNA probes: applications of the principles of nucleic acid hybridization. , 1991, Critical reviews in biochemistry and molecular biology.

[52]  G. Whitesides,et al.  Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures. , 1991, Science.

[53]  C. Siegerist,et al.  Reproducible Imaging and Dissection of Plasmid DNA Under Liquid with the Atomic Force Microscope , 1992, Science.

[54]  K. Dill,et al.  Inverse protein folding problem: designing polymer sequences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[55]  W. Shaiu,et al.  Visualization of circular DNA molecules labeled with colloidal gold spheres using atomic force microscopy , 1993 .

[56]  S A Benner,et al.  Enzymatic recognition of the base pair between isocytidine and isoguanosine. , 1993, Biochemistry.

[57]  Michael Biafore,et al.  Universal Computation in Few-body Automata , 1993, Complex Syst..

[58]  Wen-Ling Shaiu,et al.  Atomic force microscopy of oriented linear DNA molecules labeled with 5nm gold spheres , 1993, Nucleic Acids Res..

[59]  N. Seeman,et al.  DNA double-crossover molecules. , 1993, Biochemistry.

[60]  D. Millar,et al.  Conformational distributions of a four-way DNA junction revealed by time-resolved fluorescence resonance energy transfer. , 1993, Biochemistry.

[61]  N. Seeman,et al.  Construction of a DNA-Truncated Octahedron , 1994 .

[62]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[63]  N C Seeman,et al.  Cleavage of double-crossover molecules by T4 endonuclease VII. , 1994, Biochemistry.

[64]  C R Cantor,et al.  Oligonucleotide-directed self-assembly of proteins: semisynthetic DNA--streptavidin hybrid molecules as connectors for the generation of macroscopic arrays and the construction of supramolecular bioconjugates. , 1994, Nucleic acids research.

[65]  R R Breaker,et al.  A DNA enzyme that cleaves RNA. , 1994, Chemistry & biology.

[66]  Neocles B. Leontis,et al.  Bulged 3-arm DNA branched junctions as components for nanoconstruction , 1994 .

[67]  Jean-Baptiste Yunès,et al.  Seven-State Solutions to the Firing Squad Synchronization Problem , 1994, Theor. Comput. Sci..

[68]  T. S. Jayram,et al.  Efficient oblivious branching programs for threshold functions , 1994, Proceedings 35th Annual Symposium on Foundations of Computer Science.

[69]  Fred Russell Kramer,et al.  Oligonucleotide Arrays: New Concepts and Possibilities , 1994, Bio/Technology.

[70]  N C Seeman,et al.  Symmetric Holliday junction crossover isomers. , 1994, Journal of molecular biology.

[71]  Warren D. Smith DNA computers in vitro and vivo , 1995, DNA Based Computers.

[72]  Donald Beaver,et al.  A universal molecular computer , 1995, DNA Based Computers.

[73]  A. McPherson,et al.  Mechanisms of growth for protein and virus crystals , 1995, Nature Structural Biology.

[74]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[75]  W. Stemmer,et al.  Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. , 1995, Gene.

[76]  Richard J. Lipton,et al.  Breaking DES using a molecular computer , 1995, DNA Based Computers.

[77]  Paul W. K. Rothemund,et al.  A DNA and restriction enzyme implementation of Turing machines , 1995, DNA Based Computers.

[78]  Erik Winfree,et al.  Complexity of restricted and unrestricted models of molecular computation , 1995, DNA Based Computers.

[79]  Leonard M. Adleman,et al.  On constructing a molecular computer , 1995, DNA Based Computers.

[80]  N. Leontis,et al.  Refinement of the solution structure of a branched DNA three-way junction. , 1995, Biophysical journal.

[81]  Richard J. Lipton,et al.  Speeding up computations via molecular biology , 1995, DNA Based Computers.

[82]  K. Dill,et al.  Designing amino acid sequences to fold with good hydrophobic cores. , 1995, Protein engineering.

[83]  N. Kleckner,et al.  Identification of double holliday junctions as intermediates in meiotic recombination , 1995, Cell.

[84]  DNA Based Computers, Proceedings of a DIMACS Workshop, Princeton, New Jersey, USA, April 4, 1995 , 1995, DNA Based Computers.

[85]  Erik Winfree,et al.  On the computational power of DNA annealing and ligation , 1995, DNA Based Computers.

[86]  Claire Mathieu,et al.  Error-resilient DNA computation , 1996, SODA '96.

[87]  Richard J. Lipton DNA computations can have global memory , 1996, Proceedings International Conference on Computer Design. VLSI in Computers and Processors.

[88]  Max H. Garzon,et al.  Good encodings for DNA-based solutions to combinatorial problems , 1996, DNA Based Computers.

[89]  Richard J. Lipton,et al.  DNA based computers : proceedings of a DIMACS workshop, April 4, 1995, Princeton University , 1996 .

[90]  Eric Bach,et al.  DNA models and algorithms for NP-complete problems , 1996, Proceedings of Computational Complexity (Formerly Structure in Complexity Theory).

[91]  Richard J. Lipton,et al.  On the Computational Power of DNA , 1996, Discret. Appl. Math..

[92]  Erik Winfree,et al.  Universal computation via self-assembly of DNA: Some theory and experiments , 1996, DNA Based Computers.

[93]  Richard J. Lipton,et al.  DNA Based Computers , 1996 .

[94]  J. SantaLucia,et al.  Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.

[95]  P. Schultz,et al.  Organization of 'nanocrystal molecules' using DNA , 1996, Nature.

[96]  David Harlan Wood,et al.  Massively parallel DNA computation: Expansion of symbolic determinants , 1996, DNA Based Computers.

[97]  C. S. Tung,et al.  NAMOT2 - a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures , 1996, Comput. Appl. Biosci..

[98]  N. Seeman,et al.  Antiparallel DNA Double Crossover Molecules As Components for Nanoconstruction , 1996 .

[99]  J. Storhoff,et al.  A DNA-based method for rationally assembling nanoparticles into macroscopic materials , 1996, Nature.

[100]  P D Kaplan,et al.  DNA solution of the maximal clique problem. , 1997, Science.

[101]  Natasa Jonoska,et al.  Creating 3-dimensional graph structures with DNA , 1997, DNA Based Computers.

[102]  Masami Hagiya,et al.  Towards parallel evaluation and learning of Boolean μ-formulas with molecules , 1997, DNA Based Computers.

[103]  David K. Gifford,et al.  Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation , 1997, DNA Based Computers.

[104]  N C Seeman,et al.  A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT. , 1997, Journal of molecular biology.

[105]  E. Winfree Simulations of Computing by Self-Assembly , 1998 .

[106]  E. Winfree Whiplash PCR for O(1) Computing , 1998 .

[107]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[108]  E. Braun,et al.  DNA-templated assembly and electrode attachment of a conducting silver wire , 1998, Nature.

[109]  R. Landauer,et al.  Irreversibility and heat generation in the computing process , 1961, IBM J. Res. Dev..

[110]  David Thomas,et al.  The Art in Computer Programming , 2001 .

[111]  E. Winfree,et al.  Algorithmic Self-Assembly of DNA Sierpinski Triangles , 2004, PLoS biology.

[112]  E. Winfree,et al.  Design and characterization of programmable DNA nanotubes. , 2004, Journal of the American Chemical Society.

[113]  Erik Winfree,et al.  Two computational primitives for algorithmic self-assembly: copying and counting. , 2005, Nano letters.