New Generation Computing

, Volume 20, Issue 3, pp 263–277 | Cite as

DNA sequence design using templates

Special Issue

Abstract

Sequence design is a crucial problem in information-based biotechnology such as DNA-based computation. We introduce a simple strategy namedtemplate method that systematically generates a set of sequences of lengthl such that any of its member will have approximatelyl/3 mismatches with other sequences, their complements, and the overlaps of their concatenations.

Keywords

DNA Computing DNA Array Error Correcting Code 

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References

  1. 1).
    Adleman, L., “Molecular Computation of Solutions to Combinatorial Problems,”Science, 266, 5187, pp. 1021–1024, 1994.CrossRefGoogle Scholar
  2. 2).
    Allawi, H. T. and SantaLucia Jr., J., “Nearest-neighbor Thermodynamics of Internal AC Mismatches in DNA: Sequence Dependence and pH Effects,”Biochemistry, 37, 26, pp. 9435–9444, 1998.CrossRefGoogle Scholar
  3. 3).
    Ben-Dor, A., Karp, R., Schwikowski, B. and Yakhini, Z., “Universal DNA Tag Systems: A Combinatorial Design Scheme,”in Proc. of the 4th Annual International Conference on Computational Molecular Biology (RECOMB2000), ACM Press, pp. 65–75, 2000.Google Scholar
  4. 4).
    Brenner, S., “Methods for Sorting Polynucleotides using Oligonucleotide Tags,” US Patent 5604 097, 1997.Google Scholar
  5. 5).
    Deaton, R., Garzon, M. Rose, J. A., Franceschetti, D. R., Murphy, R. C. and Stevens Jr., S. E., “Reliability and Efficiency of a DNA Based Computation,”Physical Review Letters, 80, pp. 417–420, 1998.CrossRefGoogle Scholar
  6. 6).
    Frutos, A. G., Liu, Q., Thiel, A. J., Sanner, A. M. W., Condon, A. E., Smith, L. M. and Corn, R. M., “Demonstration of a Word Design Strategy for DNA Computing on Surfaces,”Nucleic Acids Research, 25, 23, pp. 4748–4757, 1997.CrossRefGoogle Scholar
  7. 7).
    Garzon, M., Neathery, P., Deaton, R., Murphy, R. C., Franceschetti, D. R. and Stevens Jr., S. E., “A New Metric for DNA Computing,”in Proc. of the 2nd Annual Genetic Programming Conference, Morgan Kaufmann, pp. 472–478, 1997.Google Scholar
  8. 8).
    Le Novere, N., “Melting, Computing the Melting Temperature of Nucleic Acid Duplex,”Bioinformatics, 17, 12, pp. 1226–1227, 2001.CrossRefGoogle Scholar
  9. 9).
    Levy, J. E., “Self-synchronizing Codes Derived From Binary Cyclic Codes,”IEEE Transactions on Information Theory, IT-12, 3, pp. 286–290, 1966.CrossRefGoogle Scholar
  10. 10).
    MacWilliams, E. J. and Sloane, N. J. A., “The Theory of Error-Correcting Codes,” North-Holland, 1977.Google Scholar
  11. 11).
    Massey, J. L., “Reversible Codes,”Information and Control, 7, pp. 369–380, 1964.MathSciNetCrossRefGoogle Scholar
  12. 12).
    Morris, M. S., Shoemaker, D. D., Davis, R. W. and Mittmann, M. P., “Methods and Compositions for Selecting Tag Nucleic Acids and Probe Arrays,” European Patent Application 97302313, 1997.Google Scholar
  13. 13).
    Nordstrom A. W. and Robinson, J. P., “An Optimum Nonlinear Codes,”Information and Control, 12, pp. 613–616, 1967.CrossRefGoogle Scholar
  14. 14).
    Sakakibara, Y. and Suyama, A., “Intelligent DNA Chips: Logical Operation of Gene Expression Profiles on DNA Computers,”in Proc. of the 11th Workshop on Genome Informatics, Universal Academy Press, pp. 33–42, 2000Google Scholar
  15. 15).
    SantaLucia, Jr., J., “A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-neighbor Thermodynamics,”in Proc. of Natl. Acad. Sci. USA, 95, pp. 1460–1465, 1998.CrossRefGoogle Scholar

Copyright information

© Ohmsha, Ltd. and Springer 2002

Authors and Affiliations

  1. 1.PRESTO, JST and Computational Biology Research CenterAISTTokyoJapan
  2. 2.Department of Computer ScienceUniversity of Electro-CommunicationsTokyoJapan

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