Advertisement

Writing Information into DNA

  • Masanori Arita
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2950)

Abstract

The time is approaching when information can be written into DNA. This tutorial work surveys the methods for designing code words using DNA, and proposes a simple code that avoids unwanted hybridization in the presence of shift and concatenation of DNA words and their complements.

Keywords

Word Design Code Word Encode Model Quaternary Code Similar Melting Temperature 
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.
    Adleman, L.M.: Molecular Computation of Solutions to Combinatorial Problems. Science 266(5187), 1021–1024 (1994)CrossRefGoogle Scholar
  2. 2.
    Brenner, S., Lerner, R.A.: Encoded Combinatorial Chemistry. Proc. Nation. Acad. Sci. USA 89(12), 5381–5383 (1992)CrossRefGoogle Scholar
  3. 3.
    Brenner, S., Williams, S.R., Vermaas, E.H., Storck, T., Moon, K., McCollum, C., Mao, J.I., Luo, S., Kirchner, J.J., Eletr, S., DuBridge, R.B., Burcham, T., Albrecht, G.: In Vitro Cloning of Complex Mixtures of DNA on Microbeads: physical separation of differentially expressed cDNAs. Proc. Nation. Acad. Sci. USA 97(4), 1665–1670 (2000)CrossRefGoogle Scholar
  4. 4.
    Ben-Dor, A., Karp, R., Schwikowski, B., Yakhini, Z.: Universal DNA Tag Systems: a combinatorial design scheme. J. Comput. Biol. 7(3-4), 503–519 (2000)CrossRefGoogle Scholar
  5. 5.
    Wong, P.C., Wong, K.-K., Foote, H.: Organic Data Memory Using the DNA Approach. Comm. of ACM 46(1), 95–98 (2003)CrossRefGoogle Scholar
  6. 6.
    Allawi, H.T., SantaLucia Jr., J.: Nearest-neighbor Thermodynamics of Internal AC Mismatches in DNA: sequence dependence and pH effects. Biochemistry 37(26), 9435–9444 (1998)CrossRefGoogle Scholar
  7. 7.
    Golomb, S.W., Gordon, B., Welch, L.R.: Comma-Free Codes. Canadian J. of Math.  10, 202–209 (1958)zbMATHMathSciNetCrossRefGoogle Scholar
  8. 8.
    Tang, B., Golomb, S.W., Graham, R.L.: A New Result on Comma-Free Codes of Even Word-Length. Canadian J. of Math. 39(3), 513–526 (1987)zbMATHMathSciNetCrossRefGoogle Scholar
  9. 9.
    Judson, H.F.: The Eighth Day of Creation: Makers of the Revolution in Biology. Cold Spring Harbor Laboratory (Original 1979; Expanded Edition 1996)Google Scholar
  10. 10.
    Stiffler, J.J.: Comma-Free Error-Correcting Codes. IEEE Trans. on Inform. Theor. IT-11, 107–112 (1965)CrossRefMathSciNetGoogle Scholar
  11. 11.
    Stiffler, J.J.: Theory of Synchronous Communication. Prentice-Hall Inc., Englewood Cliffs (1971)Google Scholar
  12. 12.
    Breslauer, K.J., Frank, R., Blocker, H., Marky, L.A.: Predicting DNA Duplex Stability from the Base Sequence. Proc. Nation. Acad. Sci. USA 83(11), 3746–3750 (1986)CrossRefGoogle Scholar
  13. 13.
    Arita, M., Kobayashi, S.: DNA Sequence Design Using Templates. New Generation Comput. 20(3), 263–277 (2002), Available as a sample paper at http://www.ohmsha.co.jp/ngc/index.htm
  14. 14.
    Zuker, M., Steigler, P.: Optimal Computer Folding of Large RNA Sequences Using Thermodynamics and Auxiliary Information. Nucleic Acids Res. 9, 133–148 (1981)CrossRefGoogle Scholar
  15. 15.
    Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular Computation: RNA Solutions to Chess Problems. Proc. Nation. Acad. Sci. USA 97(4), 1385–1389 (2000)CrossRefGoogle Scholar
  16. 16.
    Frutos, A.G., Liu, Q., Thiel, A.J., Sanner, A.M., Condon, A.E., Smith, L.M., Corn, R.M.: Demonstration of a Word Design Strategy for DNA Computing on Surfaces. Nucleic Acids Res. 25(23), 4748–4757 (1997)CrossRefGoogle Scholar
  17. 17.
    Winfree, E., Yang, X., Seeman, N.C.: Universal Computation Via Self-assembly of DNA: some theory and experiments. In: DNA Based Computers II. DIMACS Series in Discr. Math. and Theor. Comput. Sci, vol. 44, pp. 191–213 (1998)Google Scholar
  18. 18.
    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)CrossRefGoogle Scholar
  19. 19.
    Li, M., Lee, H.J., Condon, A.E., Corn, R.M.: DNA Word Design Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays. Langmuir 18(3), 805–812 (2002)CrossRefGoogle Scholar
  20. 20.
    Cattell, K., Ruskey, F., Sawada, J., Serra, M.: Fast Algorithms to Generate Necklaces, Unlabeled Necklaces, and Irreducible Polynomials over GF(2). J. Algorithms 37, 267–282 (2000)zbMATHCrossRefMathSciNetGoogle Scholar
  21. 21.
    Deaton, R., Murphy, R.C., Garzon, M., Franceschetti, D.R., Stevens Jr., S.E.: Good Encodings for DNA-based Solution to Combinatorial Problems. In: DNA Based Computers II. DIMACS Series in Discr. Math. and Theor. Comput. Sci., vol. 44, pp. 247–258 (1998)Google Scholar
  22. 22.
    Garzon, M., Neathery, P., Deaton, R., Franceschetti, D.R., Stevens Jr., S.E.: Encoding Genomes for DNA Computing. In: Proc. 3rd Annual Genet. Program. Conf., pp. 684–690. Morgan Kaufmann, San Francisco (1998)Google Scholar
  23. 23.
    Braich, R.S., Chelyapov, N., Johnson, C., Rothemund, R.W., Adleman, L.: Solution of a 20-Variable 3-SAT Problem on a DNA Computer. Science 296(5567), 499–502 (2002)CrossRefGoogle Scholar
  24. 24.
    Komiya, K., Sakamoto, K., Gouzu, H., Yokoyama, S., Arita, M., Nishikawa, A., Hagiya, M.: Successive State Transitions with I/O Interface by Molecules. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, pp. 17–26. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  25. 25.
    Tulpan, D.C., Hoos, H., Condon, A.: Stochastic Local Search ALgorithms for DNAWord Design. In: Proc. 8th Intern. Meeting on DNA-Based Computers, Sapporo, Japan, pp. 311–323 (2002)Google Scholar
  26. 26.
    MacWilliams, F.J., Sloane, N.J.A.: The Theory of Error-Correcting Codes. North-Holland, New York (1983) (2nd reprint)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Masanori Arita
    • 1
  1. 1.Department of Computational Biology, Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan

Personalised recommendations