Encyclopedia of Complexity and Systems Science

2009 Edition
| Editors: Robert A. Meyers (Editor-in-Chief)

DNA Computing

  • Martyn Amos
Reference work entry
DOI: https://doi.org/10.1007/978-0-387-30440-3_131

Definition of the Subject

DNA computing (or, more generally, biomolecular computing) is a relatively new field of study that is concerned with the use of biologicalmolecules as fundamental components of computing devices. It draws on concepts and expertise from fields as diverse as chemistry, computer science,molecular biology, physics and mathematics. Although its theoretical history dates back to the late 1950s, the notion of computing with molecules was onlyphysically realized in 1994, when Leonard Adleman demonstrated in the laboratory the solution of a small instance of a well‐known problemin combinatorics using standard tools of molecular biology. Since this initial experiment, interest in DNA computing has increased dramatically, and it isnow a well‐established area of research. As we expand our understanding of how biological and chemical systems process information,opportunities arise for new applications of molecular devices in bioinformatics, nanotechnology, engineering, the...

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Primary Literature

  1. 1.
    Adleman LM (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021–1024ADSGoogle Scholar
  2. 2.
    Adleman LM (1995) On constructing a molecular computer. Draft, University of Southern CaliforniaGoogle Scholar
  3. 3.
    Amos M (2005) Theoretical and Experimental DNA Computation. Springer, BerlinzbMATHGoogle Scholar
  4. 4.
    Amos M, Gibbons A, Hodgson D (1996) Error‐resistant implementation of DNA computations. In: Landweber LF, Baum EB (eds) 2nd Annual Workshop on DNA Based Computers. Princeton University, NJ, 10–12 June 1996. American Mathematical Society Google Scholar
  5. 5.
    Arkin A, Ross J (1994) Computational functions in biochemical reaction networks. Biophys J 67:560–578Google Scholar
  6. 6.
    Benenson Y, Adam R, Paz-Livneh T, Shapiro E (2003) DNA molecule provides a computing machine with both data and fuel. Proc Natl Acad Sci 100:2191–2196ADSGoogle Scholar
  7. 7.
    Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E (2001) Programmable and autonomous computing machine made of biomolecules. Nature 414:430–434ADSGoogle Scholar
  8. 8.
    Bennett CH (1982) The thermodynamics of computation – a review. Int J Theor Phys 21:905–940Google Scholar
  9. 9.
    Braich RS, Chelyapov N, Johnson C, Rothemund PWK, Adleman L (2002) Solution of a 20‑variable 3‑SAT problem on a DNA computer. Science 296:499–502ADSGoogle Scholar
  10. 10.
    Bray D (1995) Protein molecules as computational elements in living cells. Nature 376:307–312ADSGoogle Scholar
  11. 11.
    Breslauer KJ, Frank R, Blocker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci 83(11):3746–3750ADSGoogle Scholar
  12. 12.
    Brown TA (1993) Genetics: A Molecular Approach. Chapman and Hall, New YorkGoogle Scholar
  13. 13.
    Campbell-Kelly M, Aspray W (2004) Computer: A History of the Information Machine, 2nd edn. Westview Press, Colorado Google Scholar
  14. 14.
    Conrad M (1985) On design principles for a molecular computer. Commun ACM 28:464–480Google Scholar
  15. 15.
    Conrad M, Liberman EA (1982) Molecular computing as a link between biological and physical theory. J Theor Biol 98:239–252Google Scholar
  16. 16.
    Cook S (1971) The complexity of theorem proving procedures. Proceedings of the 3rd Annual ACM Symposium on Theory of Computing, pp 151–158Google Scholar
  17. 17.
    Faulhammer D, Cukras AR, Lipton RJ, Landweber LF (2000) Molecular computation: RNA solutions to chess problems. Proc Nat Acad Sci 97:1385–1389ADSGoogle Scholar
  18. 18.
    Feynman RP (1961) There's plenty of room at the bottom. In: Gilbert D (ed) Miniaturization. Reinhold, New York, pp 282–296Google Scholar
  19. 19.
    Garey MR, Johnson DS (1979) Computers and Intractability: A Guide to the Theory of NP‐Completeness. WH Freeman and Company, New YorkzbMATHGoogle Scholar
  20. 20.
    Gibbons AM (1985) Algorithmic Graph Theory. Cambridge University Press, CambridgezbMATHGoogle Scholar
  21. 21.
    Guarnieri F, Fliss M, Bancroft C (1996) Making DNA add. Science 273:220–223ADSGoogle Scholar
  22. 22.
    Hartmanis J (1995) On the weight of computations. Bull Euro Assoc Theor Comput Sci 55:136–138zbMATHGoogle Scholar
  23. 23.
    Hjelmfelt A, Schneider FW, Ross J (1993) Pattern recognition in coupled chemical kinetic systems. Science 260:335–337ADSGoogle Scholar
  24. 24.
    Hjelmfelt A, Weinberger ED, Ross J (1991) Chemical implementation of neural networks and Turing machines. Proc Nat Acad Sci 88:10983–10987zbMATHADSGoogle Scholar
  25. 25.
    Lipton RJ (1995) DNA solution of hard computational problems. Science 268:542–545ADSGoogle Scholar
  26. 26.
    Liu Q, Wang L, Frutos AG, Condon AE, Corn RM, Smith LM (2000) DNA computing on surfaces. Nature 403:175–179ADSGoogle Scholar
  27. 27.
    Mao C, LaBean TH, Reif JH, Seeman NC (2000) Logical computation using algorithmic self‐assembly of DNA triple‐crossover molecules. Nature 407:493–496ADSGoogle Scholar
  28. 28.
    Mullis KB, Ferré F, Gibbs RA (eds) (1994) The Polymerase Chain Reaction. Birkhauser, BostonGoogle Scholar
  29. 29.
    Ogihara M, Ray A (2000) DNA computing on a chip. Nature 403:143–144ADSGoogle Scholar
  30. 30.
    Ouyang Q, Kaplan PD, Liu S, Libchaber A (1997) DNA solution of the maximal clique problem. Science 278:446–449ADSGoogle Scholar
  31. 31.
    Regalado A (2002) DNA computing. MIT Technology Review. http://www.technologyreview.com/articles/00/05/regalado0500.asp. Accessed 26 May 2008
  32. 32.
    Rivest R, Shamir A, Adleman L (1978) A method for obtaining digital signatures and public key cryptosystems. Comm ACM 21:120–126MathSciNetzbMATHGoogle Scholar
  33. 33.
    Rothemund PWK (2006) Folding DNA to create nanoscale patterns. Nature 440:297–302ADSGoogle Scholar
  34. 34.
    Roweis S, Winfree E, Burgoyne R, Chelyapov NV, Goodman MF, Rothemund PWK, Adleman LM (1996) A sticker based architecture for DNA computation. In: Landweber LF, Baum EB (eds) 2nd Annual Workshop on DNA Based Computers. Princeton University, NJ, 10–12 June 1996. American Mathematical SocietyGoogle Scholar
  35. 35.
    Sakamoto K, Gouzu H, Komiya K, Kiga D, Yokoyama S, Yokomori T, Hagiya M (2000) Molecular computation by DNA hairpin formation. Science 288:1223–1226ADSGoogle Scholar
  36. 36.
    Smalley E (2005) Interview with Ned Seeman. Technology Research News, May 4Google Scholar
  37. 37.
    Smith LM (2006) Nanostructures: The manifold faces of DNA. Nature 440:283–284ADSGoogle Scholar
  38. 38.
    Stubbe H (1972) History of Genetics – from Prehistoric times to the Rediscovery of Mendel's Laws. MIT Press, CambridgeGoogle Scholar
  39. 39.
    van Noort D, Gast F-U, McCaskill JS (2002) DNA computing in microreactors. In: Jonoska N, Seeman NC (eds) DNA Computing: 7th International Workshop on DNA‐Based Computers. LNCS, vol 2340. Springer, Berlin, pp 33–45Google Scholar
  40. 40.
    Watkins JJ (2004) Across the Board: The Mathematics of Chess Problems. Princeton University Press, PrincetonGoogle Scholar
  41. 41.
    Watson JD, Crick FHC (1953) Genetical implications of the structure of deoxyribose nucleic acid. Nature 171:964ADSGoogle Scholar
  42. 42.
    Watson JD, Crick FHC (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737–738ADSGoogle Scholar
  43. 43.
    Watson JD, Hopkins NH, Roberts JW, Steitz JA, Weiner AM (1987) Molecular Biology of the Gene, 4th edn. Benjamin/Cummings, Menlo ParkGoogle Scholar
  44. 44.
    Winfree E, Liu F, Wenzler L, Seeman NC (1998) Design and self‐assembly of two‐dimensional DNA crystals. Nature 394:539–544ADSGoogle Scholar
  45. 45.
    Winfree E (1998) Algorithmic self‐assembly of DNA. Ph D thesis, California Institute of TechnologyGoogle Scholar
  46. 46.
    Yan H, Park SH, Finkelstein G, Reif JH, LaBean TH (2003) DNA‐templated self‐assembly of protein arrays and highly conductive nanowires. Science 301:1882–1884ADSGoogle Scholar

Books and Reviews

  1. 47.
    Adleman L (1998) Computing with DNA. Sci Am 279:54–61Google Scholar
  2. 48.
    Amos M (2006) Genesis Machines: The New Science of Biocomputing. Atlantic Books, LondonGoogle Scholar
  3. 49.
    Forbes N (2004) Imitation of Life: How Biology is Inspiring Computing. MIT Press, CambridgeGoogle Scholar
  4. 50.
    Gonick L, Wheelis M (1983) The Cartoon Guide to Genetics. Harper Perennial, New YorkGoogle Scholar
  5. 51.
    Jones R (2004) Soft Machines: Nanotechnology and Life. Oxford University Press, OxfordGoogle Scholar
  6. 52.
    Păun G, Rozenberg G, Salomaa A (1998) DNA Computing: New Computing Paradigms. Springer, BerlinGoogle Scholar
  7. 53.
    Pool R (1995) A boom in plans for DNA computing. Science 268:498–499ADSGoogle Scholar
  8. 54.
    Watson J (2004) DNA: The Secret of Life. Arrow Books, LondonGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Martyn Amos
    • 1
  1. 1.Manchester Metropolitan UniversityManchesterUK