A Proposal of DNA Computing on Beads with Application to SAT Problems

  • Takenaka Yoichi
  • Hashimoto Akihiro
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2340)


We propose a strategy using tiny beads for DNA computing. DNA computing is a means of solving intractable computation problems such as NP-complete problems. In our strategy, each bead carries multiple copies of a DNA sequence, and each sequence represents a candidate solution for a given problem. Calculation in our strategy is executed by competitive hybridization of two types of fluorescent sequences on the beads. One type of fluorescent sequences represents a constraint that has not been satisfied, and the other type a constraint that has been satisfied. After competitive hybridization, beads with only the latter type of fluorescent sequences hold “true” solutions. To extract the beads from the test tube, we use fluorescent-activated cell sorter.

We describe the approach to DNA computing on beads through SAT problems. The SAT problem is an NP-complete problem in Boolean logic. Using Megaclone, which allows DNA strands to be attached to beads, we show that DNA computing on beads can solve up to 24 variables.


Cell Sorter Boolean Logic Candidate Solution Fluorescent Sequence Competitive Hybridization 
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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Adleman, L.: Molecular computation of solutions to combinatorial problems. Science 266(11), (1994) 1021–1024CrossRefGoogle Scholar
  2. 2.
    Lipton, R.: DNA solutions of hard computation problems. Science 268(11), (1995) 542–545CrossRefGoogle Scholar
  3. 3.
    Garey, R., Johnson, S.: Computers and Intractability, a guide to the theory of NP-completeness. Freeman and Company (1991)Google Scholar
  4. 4.
    Smith L. M. et al.: A surface-based approach to DNA computation. J. Computational Biology 5, (1998) 255–267CrossRefGoogle Scholar
  5. 5.
    Liu, Q. et al.: DNA computing on surfaces. Nature 403, (2000) 175–179CrossRefGoogle Scholar
  6. 6.
    Frutos, A. G. et al.: Demonstration of a word design strategy for DNA computing on surfaces. Nucl. Acid. Res. 25, (1997) 4748–4757CrossRefGoogle Scholar
  7. 7.
    Frutos, A. G., Smith, L. M., Corn, R. M.: Enzymatic ligation reactions of DNA “words” on surfaces for DNA computing. J. Am. Chem. Soc. 120, (1998) 10277–10282CrossRefGoogle Scholar
  8. 8.
    Sakamoto, K., Gouzu, H., Komiya, K., Kiga, D., Yokoyama, S., Yokomori, T., Hagiya, M.: Molecular computation by DNA Hairpin formation. Science 288, (2000) 1223–1226CrossRefGoogle Scholar
  9. 9.
    Guanirieri, F., Fliss, M., Bancroft, C.: Making DNA add. Science 273, (1996) 220–223CrossRefGoogle Scholar
  10. 10.
    Ouyang, Q., Kaplan, P. D., Liu, S. Libchaber, A.: DNA solution of the maximal clique problem. Science 278, (1997) 446–449CrossRefGoogle Scholar
  11. 11.
    Winfee, E., Liu, F. R., Wenzler, L. A., Seeman, N. C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394, (1998) 539–544.CrossRefGoogle Scholar
  12. 12.
    Paun, G., Rozenberg, G., Salomaa, A.: DNA computing: new computing paradigms. Springer Verlag, (1998)Google Scholar
  13. 13.
    Brenner, S., et al.: Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology 18, (2000) 630–634CrossRefGoogle Scholar
  14. 14.
    Ausiello, G., Crescenzi, P., Gambosi, G., Kann, V., Marchetti-Spaccamela, A., Protasi, M.: Complexity and Approximation: combinatorial optimization problems and their approximability propoerties. Springer Verlag, (1999)Google Scholar
  15. 15.
    Brenner, S., et al.: In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. PNAS 97, (2000) 1665–1670CrossRefGoogle Scholar
  16. 16.
    Yoshida, H., Suyama, A.: Solution to 3-SAT by breadth first search. Fifth International Meeting on DNA Based Computers, (1999) 9–20Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Takenaka Yoichi
    • 1
  • Hashimoto Akihiro
    • 1
  1. 1.Department of Informatics and Mathematical ScienceOsaka UniversityOsakaJapan

Personalised recommendations