Skip to main content
Log in

DNA sequence design using templates

  • Special Issue
  • Published:
New Generation Computing Aims and scope Submit manuscript

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.

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.

Institutional subscriptions

Similar content being viewed by others

References

  1. Adleman, L., “Molecular Computation of Solutions to Combinatorial Problems,”Science, 266, 5187, pp. 1021–1024, 1994.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

  4. Brenner, S., “Methods for Sorting Polynucleotides using Oligonucleotide Tags,” US Patent 5604 097, 1997.

  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.

    Article  Google Scholar 

  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.

    Article  Google Scholar 

  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.

  8. Le Novere, N., “Melting, Computing the Melting Temperature of Nucleic Acid Duplex,”Bioinformatics, 17, 12, pp. 1226–1227, 2001.

    Article  Google Scholar 

  9. Levy, J. E., “Self-synchronizing Codes Derived From Binary Cyclic Codes,”IEEE Transactions on Information Theory, IT-12, 3, pp. 286–290, 1966.

    Article  Google Scholar 

  10. MacWilliams, E. J. and Sloane, N. J. A., “The Theory of Error-Correcting Codes,” North-Holland, 1977.

  11. Massey, J. L., “Reversible Codes,”Information and Control, 7, pp. 369–380, 1964.

    Article  MathSciNet  Google Scholar 

  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.

  13. Nordstrom A. W. and Robinson, J. P., “An Optimum Nonlinear Codes,”Information and Control, 12, pp. 613–616, 1967.

    Article  Google Scholar 

  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, 2000

  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.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Masanori Arita.

Additional information

This paper has been selected to receive the New Generation Computing Award for Distinguished Papers.

Masanori Arita, Ph.D.: He is a researcher at Computational Biology Research Center (CBRC) in National Institute of Advanced Industrial Science and Technology (AIST). He received his M.S. (1996) and Ph.D. (1999) from Department of Information Science, The University of Tokyo. He also works as a fellow of Precursory Research for Embryonic Science and Technology (PRESTO) in Japan Science and Technology Corporation (JST), and a project associate professor at Institute for Advanced Biosciences (IAB) in Keio University. Main research interests are bioinformatics and DNA computing.

Satoshi Kobayashi: He received the B.E., M.E. and D.E degrees from the University of Tokyo in 1988, 1990 and 1993, respectively. He has been an associate professor of Department of Computer Science, University of Electro-Communications since 2000 His research interests include inductive inference of formal languages, bioinformatics, and the theory of DNA computing. He is a member of ACM, Japanese Society for Artificial Intelligence (JSAI), Information Processing Society of Japan (IPSJ), and Institute of Electronics, Information and Communication Engineers, Japan (IEICE).

About this article

Cite this article

Arita, M., Kobayashi, S. DNA sequence design using templates. New Gener Comput 20, 263–277 (2002). https://doi.org/10.1007/BF03037360

Download citation

  • Received:

  • Revised:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF03037360

Keywords

Navigation