Advertisement

Programmable DNA-Based Finite Automata

  • Tamar Ratner
  • Ehud KeinanEmail author
Chapter
Part of the Natural Computing Series book series (NCS)

Abstract

Computation using DNA has many advantages, including the potential for massive parallelism that allows for large number of operations per second, the direct interface between the computation process and a biological output, and the miniaturization of the computing devices to a molecular scale. In 2001, we reported on the first DNA-based, programmable finite automaton (2-symbol-2-state) capable of computing autonomously with all its hardware, software, input, and output being soluble biomolecules mixed in solution. Later, using similar principles, we developed advanced 3-symbol-3-state automata. We have also shown that real-time detection of the output signal, as well as real-time monitoring of all the computation intermediates, can be achieved by the use of surface plasmon resonance (SPR) technology. More recently, we have shown that it is possible to achieve a biologically relevant output, such as specific gene expression, by using a reporter-gene as an output-readout. We cloned the input into circular plasmids, and thereby achieved control over gene expression by a programmable sequence of computation events. Further efforts are currently directed to immobilization of the input molecules onto a solid chip to enable parallel computation, where the location of the input on the chip represents specific tagging.

Keywords

Surface Plasmon Resonance Transition Rule Multiple Cloning Site Input Symbol Transition Molecule 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Reif JH (2002) Science 296:478–479 CrossRefGoogle Scholar
  2. 2.
    Chen J, Wood DH (2000) Proc Natl Acad Sci USA 97:1328–1330 CrossRefGoogle Scholar
  3. 3.
    Seeman NC (2003) Chem Biol 10:1151–1159 CrossRefGoogle Scholar
  4. 4.
    Shapiro E, Benenson Y (2006) Scientific American, INC 45–51 Google Scholar
  5. 5.
    Livstone S, Van Noort D, Landweber LF (2003) Molecular computing revisited: a Moore’s law? Trends Biotechnol 21:98–101 CrossRefGoogle Scholar
  6. 6.
    Ruben AJ, Landweber LF (2000) Nat Rev Mol Cell Biol 1:69–72 CrossRefGoogle Scholar
  7. 7.
    Feynman R (1961) In: Gilbert D (ed) Miniaturization. Reinhold, New York, pp 282–296 Google Scholar
  8. 8.
    Adleman LM (1994) Science 266:1021–1024 CrossRefGoogle Scholar
  9. 9.
    Lipton RJ (1995) Science 268:542–545 CrossRefGoogle Scholar
  10. 10.
    Liu Q, Wang L, Frutos AG, Condon AE, Corn RM, Smith LM (2000) Nature 403:175–179 CrossRefGoogle Scholar
  11. 11.
    Sakamoto K, Gouzu H, Komiya K, Kiga D, Yokoyama S, Yokomori T, Hagiya M (2000) Science 288:1223–1226 CrossRefGoogle Scholar
  12. 12.
    Faulhammer D, Cukras AR, Lipton RJ, Landweber LF (2000) Proc Natl Acad Sci USA 97:1385–1389 CrossRefGoogle Scholar
  13. 13.
    Braich RS, Chelyapov N, Johnson C, Rothemund PW, Adleman L (2002) Science 296:499–502 CrossRefGoogle Scholar
  14. 14.
    Roweis S, Winfree E, Burgoyne R, Chelyapov NV, Goodman MF, Rothemund PW, Adleman LM (1998) J Comput Biol 5:615–629 CrossRefGoogle Scholar
  15. 15.
    Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Nature 394:539–544 CrossRefGoogle Scholar
  16. 16.
    LaBean TH, Winfree E, Reif JH (1999) In: Winfree E, Gifford D (eds) DNA based computers V. American Mathematical Society, Cambridge, pp 123–140 Google Scholar
  17. 17.
    Winfree E (1999) J Biomol Struct Dyn, 263–270 Google Scholar
  18. 18.
    Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E (2001) Nature 414:430–434 CrossRefGoogle Scholar
  19. 19.
    Mao C, LaBean TH, Relf JH, Seeman NC (2000) Nature 407:493–496 CrossRefGoogle Scholar
  20. 20.
    Rose JA, Deaton RJ, Hagiya M, Suyama A (2002) Phys Rev E Stat Nonlinear Soft Matter Phys 65:021910 Google Scholar
  21. 21.
    Komiya K, Sakamoto K, Gouzu H, Yokoyama S, Arita M, Nishikawa A, Hagiya M (2001) In: 6th international workshop on DNA-based computers. Springer, Leiden, pp 19–26 Google Scholar
  22. 22.
    Turing AM (1936–1997) Proc Lond Math Soc 42:230–265 CrossRefGoogle Scholar
  23. 23.
    Benenson Y, Adar R, Paz-Elizur T, Livneh Z, Shapiro E (2003) Proc Natl Acad Sci USA 10:2191–2196 CrossRefGoogle Scholar
  24. 24.
    Soreni M, Yogev S, Kossoy E, Shoham Y, Keinan E (2005) J Am Chem Soc 127:3935–3943 CrossRefGoogle Scholar
  25. 25.
    Kossoy E, Lavid N, Soreni-Harari M, Shoham Y, Keinan E (2007) Chem Biol Chem 8:1255–1260 Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  1. 1.Department of ChemistryTechnion—Israel Institute of TechnologyHaifaIsrael
  2. 2.Department of Molecular Biology and The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaUSA

Personalised recommendations