Skip to main content
Log in

Theoretical and Experimental DNA Computation

Published by: Springer-Verlag, Martyn Amos 172 pages, 78 figures, 2005, ISBN-10 3-540-65773-8

  • Book Review
  • Published:
Genetic Programming and Evolvable Machines Aims and scope Submit manuscript

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

References

  1. L. Adleman, “Molecular computation of solutions of combinatorial problems,” Science, vol. 266, pp. 1021–1024, 1994.

  2. M. Arita and S. Kobayashi, “DNA sequence design using templates,” New Generation Computer, vol. 20, no. 3, pp. 263–277, 2002.

  3. Y. Benenson, T. Paz-elizur, R. Adar, E. Keinan, Z. Livneh, and E. Shapiro, “Programmable and autonomous machine made of biomolecules,” Nature, vol. 414, pp. 430–434, 2001.

  4. Y. Benenson, R. Adar, and E. Shapiro, “An autonomous molecular computer for logical control of gene expression,” Nature, vol. 429, pp. 423–429, 2004.

  5. R. S. Braich, N. Chelyapov, C. Johnson, P. W. K. Rothemund, and L. Adleman, “Solution of a 20-variable 3-SAT problem on a DNA computer,” Science, vol. 296, pp. 499–502, 2002.

  6. J. Chen and N. C. Seeman, “Synthesis from DNA of a molecule with the connectivity of a cube,” Nature, vol. 350, pp. 631–633, 1991.

  7. R. Deaton, J. Chen, H. Bi, M. Garzon, H. Rubin, and D. H. Wood, “A PCR-based protocol for in-vitro selection of non-crosshybridizing oligonucleotides,” in DNA Based Computers, M. Hagiya and A. Ohuchi (eds.), Proceedings of the Eight Annual Meeting LNCS 2568, Springer-Verlag, 2002, pp. 196–204.

  8. Z. X. Deng and C. D. Mao, “Molecular lithography with DNA nanostructures,” Angew. Chem.-Int. Ed., vol. 43, p. 4068, 2004.

  9. D. Faulhammer, A. R. Cukras, R. J. Lipton, and F. L. Landweber, “Molecular computation: RNA solutions to chess problems,” Proc. Natl. Acad. Sci. USA, vol. 97, pp. 1385–1389, 2000.

  10. M. Garzon, R. Deaton, and D. Reanult, “Virtual test tubes: a new methodology for computing,” in Proc. 7th. Int. Symposium on String Processing and Information Retrieval, A Coruňa, IEEE Computing Society Press, Spain, 2000, pp. 116–121.

  11. J. Hartmanis, “On the weight of a computation,” Bul. EATCS vol. 55, pp. 136–138, 1995.

  12. T. Head, “Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors,” Bull. Math. Biology, vol. 49, pp. 737–759, 1987.

  13. T. Head, G. Rozenberg, G. Bladregroen, C. D. K. Breek, P. H. M. Lomerese, and H. Spaink, “Computing with DNA by operating on plasmids,” BioSystems, vol. 57, pp. 87–93, 2000.

  14. S. Hussini, L. Kari, and S. Konstantinidis, “Coding properties of DNA languages,” in DNA Computing: Proceedings of the 7th International Meeting on DNA Based Computers, N. Jonoska and N. C. Seeman (eds.), LNCS 2340, Springer, 2002, pp. 57–69.

  15. N. Jonoska, P. Sa-Ardyen, and N. C. Seeman, “Computation by self-assembly of DNA graphs,” Journal of Genetic Programming And Evolvable Machines, vol. 4, pp. 123–137, 2003.

  16. P. Kaplan, G. Cecchi, and A. Libchaber, “DNA based molecular computation: template-template interactions in PCR,” in DNA Based Computers, L. Landweber and E. Baum (eds.), Proceedings of the First Annual Meeting, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 44, American Mathematical Society, Providence RI, 1998.

  17. J. Khodor and D. Gifford, “The efficiency of sequence-specific separation of DNA mixtures for biological computing,” in DNA Based Computers, H. Rubin and D. Wood (eds.), Proceedings of the Third Annual Meeting DIMACS series in Discrete Mathematical and Theoretical Computer Science, vol. 48, 1999.

  18. S. Liao and N. C. Seeman, “Translation of DNA signals into polymer assembly instructions,” Science, vol. 306, pp. 2072–2074, 2004.

  19. R. Lipton, “DNA solution of hard computational problems,” Science, vol. 268, pp. 542–545, 1995.

  20. A. Marathe, A. E. Condon, and R. M. Corn, “On combinatorial word design,” in Preproceedings of the 5th International Meeting on DNA Based Computers, Boston, 1999, pp. 75–88.

  21. M. Ogihara and A. Ray, “Simulating Boolean circuits on a DNA computer,” in Proc. of the First Annual International Conference on Computational Molecular Biology (RECOMB97), ACM Press, 1997, pp. 226–231.

  22. Gh. Păun, G. Rozenberg, and A. Salomaa, DNA Computing, New Computing Paradigms, Springer Verlag, 1998.

  23. P. W. K. Rothemund, N. Papadakis, and E. Winfree, “Algorithmic self-assembly of DNA Sierpinsky triangles,” PLoS Biology, vol. 2, no. 12, 2004, 13 pp. e424.

  24. P. W. K. Rothemund, “Scaffolded DNA origami: From generalized multicrossovers to polygonal networks,” in Nanotechnology: Science and Computation, J. Chen, N. Jonoska, and G. Rozenberg (eds.), 2006, pp. 1–21.

  25. P. W. K. Rothemund, “Folding DNA to create nanoscale shapes and patterns,” Nature, vol. 440, pp. 297–302, 2006.

  26. Y. Sakakibara, “Development of a bacteria computer: From in silico finite automata to in vitro and in vivo,” Bulletin of EATCS, vol. 87, pp. 165–178, 2005.

  27. N. C. Seeman, “DNA in a material world,” Nature, vol. 421, p. 427, 2003.

  28. B. Yurke, A. J. Turberfield, A. P. Mills, and F. C. Simmel Jr., “A DNA fueled molecular machine made of DNA,” Nature, vol. 406, pp. 605–608, 2000.

Download references

Acknowledgments

The author thanks W.B. Langdon for many helpful remarks.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nataša Jonoska.

Additional information

ACM Computing Classification (1998): F, 1-2, G.2.1-2, J.3.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jonoska, N. Theoretical and Experimental DNA Computation. Genet Program Evolvable Mach 7, 287–291 (2006). https://doi.org/10.1007/s10710-006-9011-9

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10710-006-9011-9

Keywords

Navigation