Skip to main content

Towards Evolutionary DNA Computing

  • Conference paper
Mechanisms, Symbols, and Models Underlying Cognition (IWINAC 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3561))

  • 623 Accesses

Abstract

In the last decade, the implementation of computations using DNA has attracted a lot of attention from both computer scientists and biologists. Molecular computation has many advantages, including small size, a biological interface and massive parallelism. This potential offers interesting possibilities for the implementation of evolutionary computation using DNA. We discuss the potential of evolutionary DNA computing and experimental progress.

Invited paper.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Păun, G., Rozenberg, G., Salomaa, A.: DNA Computing: New Computing Paradigms. Springer, Heidelberg (1998)

    MATH  Google Scholar 

  2. Adleman, L.M.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1024 (1994)

    Article  Google Scholar 

  3. Schneider, T.D.: Theory of Molecular Machines. II. Energy Dissipation from Molecular Machines. J. Theor. Biol. 148, 125–137 (1991)

    Article  Google Scholar 

  4. Ouyang, Q., Kaplan, P.D., Liu, S.M., Libchaber, A.: DNA Solution of the Maximal Clique Problem. Science 278, 446–449 (1997)

    Article  Google Scholar 

  5. Yoshida, H., Suyama, A.: Solution to 3-SAT by Breadth First Search. In: WInfree, E., Gifford, D.K. (eds.) DNA Based Computers V, pp. 9–22. American Mathematical Society, Providence, RI (2000)

    Google Scholar 

  6. Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular Computation: RNA Solutions to Chess Problems. Proc. Natl. Acad. Sci. USA 91, 1385–1389 (2000)

    Article  Google Scholar 

  7. Head, T., Rozenberg, G., Bladergroen, R.S., Breek, C.K.D., Lommerse, P.H.M., Spaink, H.P.: Computing with DNA by Operating on Plasmids. Biosystems 57, 87–93 (2000)

    Article  Google Scholar 

  8. Liu, Q., Wang, L., Frutos, A.G., Condon, A.E., Corn, R.M., Smith, L.M.: DNA Computing on Surfaces. Nature 403, 175–179 (2000)

    Article  Google Scholar 

  9. Sakamoto, K., Gouzu, H., Komiya, K., Kiga, D., Yokoyama, S., Yokomore, T., Hagiya, M.: Molecular Computation by DNA Hairpin Formation. Science 288, 1223–1226 (2000)

    Article  Google Scholar 

  10. Wang, L., Hall, J.G., Lu, M., Liu, Q., Smith, L.M.: A DNA Computing Readout Operation Based on Structure-Specific Cleavage. Nat. Biotechnol. 19, 1053–1059 (2001)

    Article  Google Scholar 

  11. Braich, R.S., Chelyapov, N., Johnson, C., Rothemund, P.W.K., Adleman, L.: Solution to a 20-Variable 3-SAT Problem on a DNA Computer. Science 296, 499–502 (2002)

    Article  Google Scholar 

  12. Schmidt, K.A., Henkel, C.V., Rozenberg, G., Spaink, H.P.: DNA Computing Using Single-Molecule Hybridization Detection. Nucleic Acids Res. 32, 4962–4968 (2004)

    Article  Google Scholar 

  13. Ogihara, M., Ray, A.: DNA-Based Parallel Computing by ’Counting’. In: Rubin, H., Wood, D.H. (eds.) DNA Based Computers III: DIMACS Workshop, pp. 265–274. American Mathematical Society, Providence, RI (1997)

    Google Scholar 

  14. Lipton, R.J.: DNA Solution of Hard Computational Problems. Science 268, 542–545 (1995)

    Article  Google Scholar 

  15. Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N.V., Goodman, M.F., Adleman, L.M., Rothemund, P.W.K.: A Sticker-Based Model for DNA Computation. J. Comput. BIol. 5, 615–629 (1998)

    Article  Google Scholar 

  16. Rozenberg, G., Spaink, H.: DNA Computing by Blocking. Theor. Comput. Sci. 292, 653–665 (2003)

    Article  MATH  MathSciNet  Google Scholar 

  17. Henkel, C.V.: Experimental DNA Computing. PhD thesis, Leiden University (2005)

    Google Scholar 

  18. Mauri, G., Ferretti, C.: Word Design for Molecular Computing: a Survey. In: Chen, J., Reif, J. (eds.) DNA Computing, 9th International Workshop on DNA Based Computers, pp. 37–47. Springer, Heidelberg (2004)

    Google Scholar 

  19. Heldkamp, U., Rauhe, H., Banzhaf, W.: Software Tools for DNA Sequence Design. Genetic Programming and Evolvable Machines 4, 153–171 (2003)

    Article  Google Scholar 

  20. Hagiya, M.: From Molecular Computing to Molecular Programming. In: Condon, A., Rozenberg, G. (eds.) DNA Computing, 6th International Workshop on DNA-Based Computers, pp. 89–102. Springer, Heidelberg (2001)

    Google Scholar 

  21. Gehani, A., Reif, J.: Micro Flow Bio-Molecular Computation. Biosystems 52, 197–216 (1999)

    Article  Google Scholar 

  22. McCaskill, J.S.: Optically Programming DNA Computing in Microflow Reactors. Biosystems 59, 125–138 (2001)

    Article  Google Scholar 

  23. Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and Autonomous Computing Machine Made of Biomolecules. Nature 414, 430–434 (2001)

    Article  Google Scholar 

  24. Stemmer, W.P.C.: The Evolution of Molecular Computation. Science 270, 1510 (1995)

    Article  Google Scholar 

  25. Adleman, L.M.: On Constructing a Molecular Computer. In: Lipton, R.J., Baum, E. (eds.) DNA Based Computers, DIMACS 27, pp. 1–21. American Mathematical Society, Providence, RI (1996)

    Google Scholar 

  26. Deaton, R., Murphy, R.C., Rose, J.A., Garzon, M., Franschetti, D.R., Stevens Jr., S.E.: A DNA Based Implementation of an Evolutionary Search for Good Encodings for DNA Computation. In: Proceedings of the Fourth IEEE Conference on Evolutionary Computation, Indianapolis, IN, pp. 267–271. IEEE Press, Piscataway (1997)

    Google Scholar 

  27. Chen, J., Wood, D.H.: Computation with Biomolecules. Proc. Natl. Acad. Sci. USA 97, 1328–1330 (2000)

    Article  Google Scholar 

  28. Bäck, T., Kok, J.N., Rozenberg, G.: Evolutionary Computation as a Paradigm for DNA-Based Computation. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation. DIMACS Workshop, Princeton, pp. 15–40. Springer, Heidelberg (2003)

    Google Scholar 

  29. Nuser, M., Deaton, R.: Simulations of DNA Computing with In Vitro Selection. Genetic Programming and Evolvable Machines 4, 173–183 (2003)

    Article  Google Scholar 

  30. Stemmer, W.P.C.: Rapid Evolution of a Protein In Vitro by DNA Shuffling. Nature 370, 389–391 (1994)

    Article  Google Scholar 

  31. Minshull, J., Stemmer, W.P.C.: Protein Evolution by Molecular Breeding. Curr. Opin. Chem. Biol. 3, 284–290 (1999)

    Article  Google Scholar 

  32. Joyce, G.F.: Directed Evolution of Nucleic Acid Enzymes. Annu. Rev. Biochem. 73, 791–836 (2004)

    Article  Google Scholar 

  33. Nataraj, A.J., Olivos-Glander, I., Kusukawa, N., Highsmith, W.E.: Single-Strand Conformation Polymorphism an Heteroduplex Analysis for Gel-Based Mutation Detection. Electrophoresis 20, 1177–1185 (1999)

    Article  Google Scholar 

  34. Wood, D., Chen, J., Antipov, E., Lemieux, B., Cedeno, W.: A DNA Implementation of the Max 1s Problem. In: Banzhaf, W., Eiben, A.E., Garzon, M.H., Honavar, V., Jakiela, M., Smith, R.E. (eds.) Proceedings of the Genetic and Evolutionary Computation Conference 1999, pp. 1835–1841. Morgan Kaufman, San Francisco (1999)

    Google Scholar 

  35. Goode, E., Wood, D.H., Chen, J.: DNA Implementation of a Royal Road Fitness Evaluation. In: Condon, A., Rozenberg, G. (eds.) DNA Computing, Proceedings 6th International Workshop on DNA-Based Computers, pp. 247–262. Springer, Heidelberg (2001)

    Google Scholar 

  36. Henkel, C.V., Rozenberg, G., Spaink, H.P.: Application of Mismatch Detection Methods in DNA Computing. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA10, Tenth International Meeting on DNA Computing, Preliminary Proceedings, Università di Milano-Bicocca, pp. 183–192 (2004)

    Google Scholar 

  37. Loakes, D.: The Application of Universal DNA Base Analogues. Nucleic Acids Res. 29, 2437–2447 (2001)

    Article  Google Scholar 

  38. Gottlieb, J., Marchiori, E., Rossi, C.: Evolutionary Algorithms for the Satisfiability Problem. Evol. Comput. 10, 35–50 (2002)

    Article  Google Scholar 

  39. Upchurch, D.A., Shankarappa, R., Mullins, J.I.: Position and Degree of Mismatches and the Mobility of DNA Heteroduplexes. Nucleic Acids Res. 69, e69 (2000)

    Google Scholar 

  40. Fraenkel, A.S.: Protein Folding, Spin Glass and Computational Complexity. In: Rubin, H., Wood, D.H. (eds.) DNA Based Computers III, Proceedings DIMACS Workshop, pp. 101–121. American Mathematical Society, Providence (1999)

    Google Scholar 

  41. Pierce, N.A., Winfree, E.: Protein Design is NP-Hard. Protein Eng. 15, 779–782 (2002)

    Article  Google Scholar 

  42. Deaton, R., Chen, J., Bi, H., Rubin, H., Wood, D.H.: A PCR-Based Protocol for In Vitro Selection of Non-Crosshybridizing Oligonucleotides. In: Hagiya, M., Ohuchi, A. (eds.) DNA Computing, 8th International Workshop on DNA-Based Computers, pp. 196–204. Springer, Heidelberg (2003)

    Google Scholar 

  43. Chen, J., Deaton, R., Garzon, M., Kim, J.W., Wood, D., Bi, H., Carpenter, D., Wang, Y.Z.: Characterization of Non-Crosshybridizing DNA Oligonucleotides Manufactured In Vitro. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA10, Tenth International Meeting on DNA Computing, Preliminary Proceedings, Università di Milano-Bicocca, pp. 132–141 (2004)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Henkel, C.V., Kok, J.N. (2005). Towards Evolutionary DNA Computing. In: Mira, J., Álvarez, J.R. (eds) Mechanisms, Symbols, and Models Underlying Cognition. IWINAC 2005. Lecture Notes in Computer Science, vol 3561. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11499220_26

Download citation

  • DOI: https://doi.org/10.1007/11499220_26

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-26298-5

  • Online ISBN: 978-3-540-31672-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics