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Programmable DNA-Based Finite Automata

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Algorithmic Bioprocesses

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

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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.

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References

  1. Reif JH (2002) Science 296:478–479

    Article  Google Scholar 

  2. Chen J, Wood DH (2000) Proc Natl Acad Sci USA 97:1328–1330

    Article  Google Scholar 

  3. Seeman NC (2003) Chem Biol 10:1151–1159

    Article  Google Scholar 

  4. Shapiro E, Benenson Y (2006) Scientific American, INC 45–51

    Google Scholar 

  5. Livstone S, Van Noort D, Landweber LF (2003) Molecular computing revisited: a Moore’s law? Trends Biotechnol 21:98–101

    Article  Google Scholar 

  6. Ruben AJ, Landweber LF (2000) Nat Rev Mol Cell Biol 1:69–72

    Article  Google Scholar 

  7. Feynman R (1961) In: Gilbert D (ed) Miniaturization. Reinhold, New York, pp 282–296

    Google Scholar 

  8. Adleman LM (1994) Science 266:1021–1024

    Article  Google Scholar 

  9. Lipton RJ (1995) Science 268:542–545

    Article  Google Scholar 

  10. Liu Q, Wang L, Frutos AG, Condon AE, Corn RM, Smith LM (2000) Nature 403:175–179

    Article  Google Scholar 

  11. Sakamoto K, Gouzu H, Komiya K, Kiga D, Yokoyama S, Yokomori T, Hagiya M (2000) Science 288:1223–1226

    Article  Google Scholar 

  12. Faulhammer D, Cukras AR, Lipton RJ, Landweber LF (2000) Proc Natl Acad Sci USA 97:1385–1389

    Article  Google Scholar 

  13. Braich RS, Chelyapov N, Johnson C, Rothemund PW, Adleman L (2002) Science 296:499–502

    Article  Google Scholar 

  14. Roweis S, Winfree E, Burgoyne R, Chelyapov NV, Goodman MF, Rothemund PW, Adleman LM (1998) J Comput Biol 5:615–629

    Article  Google Scholar 

  15. Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Nature 394:539–544

    Article  Google Scholar 

  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. Winfree E (1999) J Biomol Struct Dyn, 263–270

    Google Scholar 

  18. Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E (2001) Nature 414:430–434

    Article  Google Scholar 

  19. Mao C, LaBean TH, Relf JH, Seeman NC (2000) Nature 407:493–496

    Article  Google Scholar 

  20. Rose JA, Deaton RJ, Hagiya M, Suyama A (2002) Phys Rev E Stat Nonlinear Soft Matter Phys 65:021910

    Google Scholar 

  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. Turing AM (1936–1997) Proc Lond Math Soc 42:230–265

    Article  Google Scholar 

  23. Benenson Y, Adar R, Paz-Elizur T, Livneh Z, Shapiro E (2003) Proc Natl Acad Sci USA 10:2191–2196

    Article  Google Scholar 

  24. Soreni M, Yogev S, Kossoy E, Shoham Y, Keinan E (2005) J Am Chem Soc 127:3935–3943

    Article  Google Scholar 

  25. Kossoy E, Lavid N, Soreni-Harari M, Shoham Y, Keinan E (2007) Chem Biol Chem 8:1255–1260

    Google Scholar 

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Correspondence to Ehud Keinan .

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Ratner, T., Keinan, E. (2009). Programmable DNA-Based Finite Automata. 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_25

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  • DOI: https://doi.org/10.1007/978-3-540-88869-7_25

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  • Print ISBN: 978-3-540-88868-0

  • Online ISBN: 978-3-540-88869-7

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