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Algorithmic Bioprocesses pp 215–225Cite as

Algorithmic Control: The Assembly and Operation of DNA Nanostructures and Molecular Machinery

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Part of the book series: Natural Computing Series ((NCS))

Abstract

It gives me great pleasure to contribute to this celebration of Grzegorz Rozenberg’s contribution to the field of natural computing. I am grateful to Grzegorz for fostering this remarkably interdisciplinary community which has provided me with so much interest and enjoyment.

The theme of this symposium is ‘algorithmic bioprocesses’: this paper is concerned with the creation of artificial structures by algorithmic assembly of a biomolecule, DNA. I will survey different strategies for encoding assembly and operation algorithms in the design of DNA nanostructures, using examples that my colleagues and I have worked on.

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References

  1. The Oxford English Dictionary (1989) 2nd edn. Oxford University Press

    Google Scholar 

  2. Watson JD, Crick FHC (1953) A structure for deoxyribose nucleic acid. Nature 171:737–738

    Article  Google Scholar 

  3. Gilbert DE, Feigon J (1999) Multistranded DNA structures. Curr Opin Struct Biol 9:305–314

    Article  Google Scholar 

  4. Seeman NC (2003) DNA in a material world. Nature 421:427–431

    Article  MathSciNet  Google Scholar 

  5. Seeman NC (1990) De novo design of sequences for nucleic-acid structural engineering. J Biomol Struc Dyn 8:573–581

    Google Scholar 

  6. Dirks RM, Lin M, Winfree E, Pierce NA (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res 32:1392–1403

    Article  Google Scholar 

  7. Goodman RP (2005) NANEV: a program employing evolutionary methods for the design of nucleic acid nanostructures. Biotechniques 38:548–550

    Article  Google Scholar 

  8. Goodman RP, Schaap IAT, Tardin CF, Erben CM, Berry RM, Schmidt CF, Turberfield AJ (2005) Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310:1661–1665

    Article  Google Scholar 

  9. Smith SB, Finzi L, Bustamante C (1992) Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258:1122–1126

    Article  Google Scholar 

  10. Shih WM, Quispe JD, Joyce GF (2004) A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427:618–621

    Article  Google Scholar 

  11. Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:298–302

    Article  Google Scholar 

  12. Chen JH, Seeman NC (1991) Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350:631–633

    Article  Google Scholar 

  13. Zhang YW, Seeman NC (1994) Construction of a DNA-truncated octahedron. J Am Chem Soc 116:1661–1669

    Article  Google Scholar 

  14. Fu TJ, Seeman NC (1993) DNA double-crossover molecules. Biochemistry 32:3211–3220

    Article  Google Scholar 

  15. Winfree E, Liu FR, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544

    Article  Google Scholar 

  16. Mao CD, Sun WQ, Seeman NC (1999) Designed two-dimensional DNA Holliday junction arrays visualized by atomic force microscopy. J Am Chem Soc 121:5437–5443

    Article  Google Scholar 

  17. LaBean TH, Yan H, Kopatsch J, Liu FR, Winfree E, Reif JH, Seeman NC (2000) Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J Am Chem Soc 122:1848–1860

    Article  Google Scholar 

  18. Yan H, Park SH, Finkelstein G, Reif JH, LaBean TH (2003) DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301:1882–1884

    Article  Google Scholar 

  19. Malo J, Mitchell JC, Venien-Bryan C, Harris JR, Wille H, Sherratt DJ, Turberfield AJ (2005) Engineering a 2D protein-DNA crystal. Angew Chem Int Ed 44:3057–3061

    Article  Google Scholar 

  20. He Y, Chen Y, Liu HP, Ribbe AE, Mao CD (2005) Self-assembly of hexagonal DNA two-dimensional (2D) arrays. J Am Chem Soc 127:12202–12203

    Article  Google Scholar 

  21. He Y, Tian Y, Ribbe AE, Mao CD (2006) Highly connected two-dimensional crystals of DNA six-point-stars. J Am Chem Soc 128:15978–15979

    Article  Google Scholar 

  22. Ortiz-Lombardia M, Gonzalez A, Eritja R, Aymami J, Azorin F, Coll M (1999) Crystal structure of a DNA Holliday junction. Nat Struct Biol 6:913–917

    Article  Google Scholar 

  23. Eichman BF, Vargason JM, Mooers BH, Ho PS (2000) The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Proc Natl Acad Sci USA 97:3971–3976

    Article  Google Scholar 

  24. Syôzi I (1951) Statistics of Kagomé lattice. Prog Theor Phys 6:306–308

    Article  MATH  Google Scholar 

  25. Zerbib D, Mezard C, George H, West SC (1998) Coordinated actions of RuvABC in holliday junction processing. J Mol Biol 281:621–630

    Article  Google Scholar 

  26. Winfree E (1996) On the computational power of DNA annealing and ligation. In: Lipton RJ, Baum EB (eds) DNA based computers, vol 27. American Mathematical Society, Providence, pp 199–221

    Google Scholar 

  27. Mao C, LaBean TH, Reif JH, Seeman NC (2000) Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407:493–496

    Article  Google Scholar 

  28. Rothemund PWK, Papadakis N, Winfree E (2004) Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol 2:2041–2053

    Article  Google Scholar 

  29. Barish RD, Rothemund PWK, Winfree E (2005) Two computational primitives for algorithmic self-assembly: copying and counting. Nano Lett 12:2586–2592

    Article  Google Scholar 

  30. Winfree E, Bekbolatov R (2004) Proofreading tile sets: error correction for algorithmic self-assembly. DNA Comput 2943:126–144

    MathSciNet  Google Scholar 

  31. Turberfield AJ, Mitchell JC, Yurke B, Mills AP, Blakey MI, Simmel FC (2003) DNA fuel for free-running nanomachines. Phys Rev Lett 90:118102

    Article  Google Scholar 

  32. Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, Pierce NA (2005) Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res 33:4090–4095

    Article  Google Scholar 

  33. Seelig G, Yurke B, Winfree E (2006) Catalysed relaxation of a metastable fuel. J Am Chem Soc 128:12211–12220

    Article  Google Scholar 

  34. Green SJ, Lubrich D, Turberfield AJ (2006) DNA hairpins: fuel for autonomous DNA devices. Biophys J 91:2966–2975

    Article  Google Scholar 

  35. Dirks RM, Pierce NA (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci USA 101:15275–15278

    Article  Google Scholar 

  36. Yin P, Choi HMT, Calvert CR, Pierce NA (2008) Programming biomolecular self-assembly pathways. Nature 451:318–323

    Article  Google Scholar 

  37. Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314:1585–1588

    Article  Google Scholar 

  38. Zhang DY, Turberfield AJ, Yurke B, Winfree E (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121–1125

    Article  Google Scholar 

  39. Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605–608

    Article  Google Scholar 

  40. Yan H, Zhang X, Shen Z, Seeman NC (2002) A robust DNA mechanical device controlled by hybridization topology. Nature 415:62–65

    Article  Google Scholar 

  41. Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ (2008) Reconfigurable, braced, three-dimensional DNA nanostructures. Nat Nanotechnol 3:93–96

    Article  Google Scholar 

  42. Erben CM, Goodman RP, Turberfield AJ (2006) Single-molecule protein encapsulation in a rigid DNA cage. Angew Chem Int Ed 45:7414–7417

    Article  Google Scholar 

  43. Liao S, Seeman NC (2004) Translation of DNA signals into polymer assembly instructions. Science 306:2072–2074

    Article  Google Scholar 

  44. Chen Y, Mao C (2004) Reprogramming DNA-directed reactions on the basis of a DNA conformational change. J Am Chem Soc 126:13240–13241

    Article  Google Scholar 

  45. Snyder TM, Liu DR (2005) Ordered multistep synthesis in a single solution directed by DNA templates. Angew Chem Int Ed 44:7379–7382

    Article  Google Scholar 

  46. Chhabra R, Sharma J, Liu Y, Yan H (2006) Addressable molecular tweezers for DNA-templated coupling reactions. Nano Lett 6:978–983

    Article  Google Scholar 

  47. Sherman WB, Seeman NC (2004) A precisely controlled DNA biped walking device. Nano Lett 4:1203–1207

    Article  Google Scholar 

  48. Shin J-S, Pierce NA (2004) A synthetic DNA walker for molecular transport. J Am Chem Soc 126:10834–10835

    Article  Google Scholar 

  49. Mao C, Sun W, Shen Z, Seeman NC (1999) A nanomechanical device based on the B–Z transition of DNA. Nature 397:144–146

    Article  Google Scholar 

  50. Liu D, Balasubramanian S (2003) A proton-fuelled DNA nanomachine. Angew Chem Int Ed 42:5734–5736

    Article  Google Scholar 

  51. Alberti P, Mergny J-L (2003) DNA duplex–quadruplex exchange as the basis for a nanomolecular machine. Proc Natl Acad Sci USA 100:1569–1573

    Article  Google Scholar 

  52. Liedl T, Simmel FC (2005) Switching the conformation of a DNA molecule with a chemical oscillator. Nano Lett 5:1894–1898

    Article  Google Scholar 

  53. Dittmer WU, Simmel FC (2004) Transcriptional control of DNA-based nanomachines. Nano Lett 4:689–691

    Article  Google Scholar 

  54. Bath J, Turberfield AJ (2007) DNA nanomachines. Nat Nanotechnol 2:275–284

    Article  Google Scholar 

  55. SantaLucia J (1998) A unified view of polymer, dumbell, and oligonucleotide nearest neighbour thermodynamics. Proc Natl Acad Sci USA 95:1460–1465

    Article  Google Scholar 

  56. Yin P, Yan H, Daniell XG, Turberfield AJ, Reif JH (2004) A unidirectional DNA walker that moves autonomously along a DNA track. Angew Chem Int Ed 43:4906–4911

    Article  Google Scholar 

  57. Bath J, Green SJ, Turberfield AJ (2005) A free-running DNA motor powered by a nicking enzyme. Angew Chem Int Ed 44:4358–4361

    Article  Google Scholar 

  58. Tian Y, He Y, Peng Y, Mao C (2005) A DNA enzyme that walks processively and autonomously along a one-dimensional track. Angew Chem Int Ed 44:4355–4358

    Article  Google Scholar 

  59. Pei R, Taylor SK, Stefanovic D, Rudchenko S, Mitchell TE, Stojanovic MN (2006) Behavior of polycatalytic assemblies in a substrate-displaying matrix. J Am Chem Soc 128:12693–12699

    Article  Google Scholar 

  60. Heiter DF, Lunnen KD, Wilson GG (2005) Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R. BbvCI J Mol Biol 348:631–640

    Article  Google Scholar 

  61. Lee CS, Davis RW, Davidson N (1970) A physical study by electron microscopy of the terminally repetitious, circularly permuted DNA from the coliphage particles of Escherichia coli 15. J Mol Biol 48:1–8

    Article  Google Scholar 

  62. Yurke B, Mills AP (2003) Using DNA to power nanostructures. Genet Program Evol Mach 4:111–122

    Article  Google Scholar 

  63. Venkataraman S, Dirks RM, Rothemund PWK, Winfree E, Pierce NA (2007) An autonomous polymerization motor powered by DNA hybridization. Nat Nanotechnol 2:490–494

    Article  Google Scholar 

  64. Yin P, Turberfield AJ, Reif JH (2005) Designs of autonomous unidirectional walking DNA devices. DNA Comput 3384:410–425

    Article  MathSciNet  Google Scholar 

  65. Green SJ, Bath J, Turberfield AJ (2008) Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. Phys Rev Lett 101:238101

    Article  Google Scholar 

  66. Bath J, Green SJ, Allen KE, Turberfield AJ (2009) Mechanism for a directional, processive, and reversible DNA motor. Small (in press)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK

    Andrew J. Turberfield

Authors
  1. Andrew J. Turberfield
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Correspondence to Andrew J. Turberfield .

Editor information

Editors and Affiliations

  1. Dept. Computer Science, University of British Columbia, Main Mall 201-2366, Vancouver, V6T 1Z4, Canada

    Anne Condon

  2. Dept. Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel

    David Harel

  3. Leiden Inst. Advanced Computer Science, Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, Netherlands

    Joost N. Kok

  4. Turku Centre for Computer Science, Lemminkaisenkatu 14 A, Turku, 20520, Finland

    Arto Salomaa

  5. Computer Science, Computation,, California Inst. of Technology, Pasadena, 91125, U.S.A.

    Erik Winfree

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© 2009 Springer-Verlag Berlin Heidelberg

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Turberfield, A.J. (2009). Algorithmic Control: The Assembly and Operation of DNA Nanostructures and Molecular Machinery. In: Condon, A., Harel, D., Kok, J., Salomaa, A., Winfree, E. (eds) Algorithmic Bioprocesses. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88869-7_13

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  • DOI: https://doi.org/10.1007/978-3-540-88869-7_13

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-88868-0

  • Online ISBN: 978-3-540-88869-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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