Nothing Special   »   [go: up one dir, main page]
Skip to main content
Springer Nature Link
Log in

Software Tools for DNA Sequence Design

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

Abstract

The design of DNA sequences is a key problem for implementing molecular self-assembly with nucleic acid molecules. These molecules must meet several physical, chemical and logical requirements, mainly to avoid mishybridization. Since manual selection of proper sequences is too time-consuming for more than a handful of molecules, the aid of computer programs is advisable. In this paper two software tools for designing DNA sequences are presented, the DNASequenceGenerator and the DNASequenceCompiler. Both employ an approach of sequence dissimilarity based on the uniqueness of overlapping subsequences and a graph based algorithm for sequence generation. Other sequence properties like melting temperature or forbidden subsequences are also regarded, but not secondary structure errors or equilibrium chemistry. Fields of application are DNA computing and DNA-based nanotechnology. In the second part of this paper, sequences generated with the DNASequenceGenerator are compared to those from several publications of other groups, an example application for the DNASequenceCompiler is presented, and the advantages and disadvantages of the presented approach are discussed.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Explore related subjects

Discover the latest articles, news and stories from top researchers in related subjects.

References

  1. M. Arita, A. Nishikawa, M. Hagiya, K. Komiya, and H. Gouzu, K. Sakamoto, “Improving sequence design for DNA computing,” in Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2000), D. Whitley, et al. (eds.), Morgan Kaufmann, 2000, pp. 875-882.

  2. E. B. Baum, “DNA sequences useful for computation,” unpublished, available under http://www.neci.nj.nec.com/homepages/eric/seq.ps, 1996.

  3. A. Ben-Dor, R. Karp, B. Schwikowski, and Z. Yakhini, “Universal DNA tag systems: A combinatorial design scheme,” Journal of Computational Biology, vol. 7, pp. 503-519, 2000.

    Article  Google Scholar 

  4. A. Brenneman and A. E. Condon, “Strand design for bio-molecular computation”, to appear, available at http://www.cs.ubc.ca/~condon/papers/wordsurvey.ps, 2001.

  5. S. Brenner, “Methods for sorting polynucleotides using oligonucleotide tags,” US Patent 5,604,097, 1997.

  6. K. J. Breslauer, R. Frank, and H. Blöcker, “Predicting DNA duplex stability from the base sequence,” Proceedings of the National Acadamy of Sciences, vol. 83, pp. 3746-3750, 1986.

    Article  Google Scholar 

  7. 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.

    Article  Google Scholar 

  8. R. Deaton, J. Chen, H. Bi, and J. A. Rose, “A software tool for generating non-crosshybridizing libraries of DNA oligonucleotides,” in Preliminary Proceedings of the 8th International Meeting on DNA Based Computers, June 10–13 2002, Hokkaido University, 2003, pp. 211-220.

  9. R. Deaton, R. C. Murphy, M. Garzon, D. T. Franceschetti, and E. Stevens Jr., “Good encodings for DNA-based solutions to combinatorial problems,” in Proceedings of the Second Annual Meeting on DNA Based Computers, held at Princeton University, 1996, pp. 159-171.

  10. R. Deaton, R. C. Murphy, J. A. Rose, M. Garzon, D. T. Franceschetti, and S. E. Stevens Jr., “Genetic search for reliable encodings for DNA-based computation,” in First Conference on Genetic Programming, 1996.

  11. D. Faulhammer, A. R. Cukras, R. J. Lipton, and L. F. Landweber, “Molecular computation: RNA solutions to chess problems,” Proceedings of the National Academy of Sciences, vol. 97, pp. 1385-1389, 2000.

    Article  Google Scholar 

  12. U. Feldkamp, W. Banzhaf, and H. Rauhe, “A DNA sequence compiler,” in Preliminary Proceedings of the 6th DIMACS Workshop on DNA Based Computers, held at the University of Leiden, The Netherlands: p. 253, 2000. Manuscript available at: http://LS11-www.cs.uni-dortmund.de/molcomp/Publications/publications.html.

  13. U. Feldkamp, S. Saghafi, W. Banzhaf, and H. Rauhe, “DNASequenceGenerator: A program for the construction of DNA sequences,” DNA Computing, 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A., 10–13, June 2001 pp. 23-32, 2001

  14. A. G. Frutos, Q. Liu, A. J. Thiel, A. M. W. Sanner, A. E. Condon, L. M. Smith, and R. M. Corn, “Demonstration of a word design strategy for DNA computing on surfaces,” Nucleic Acids Research, vol. 25, pp. 4748-4757, 1997.

    Article  Google Scholar 

  15. M. Garzon, R. Deaton, P. Neathery, D. R. Franceschetti, and R. C. Murphy, “A new metric for DNA computing,” in Conference on Genetic Programming, GP-97, Stanford University: Stanford, California, J. R. Koza et al. (eds.), 1997.

  16. M. Garzon, R. J. Deaton, J. A. Rose, and D. R. Franceschetti, “Soft molecular computing,” in Proceedings 5th DIMACS Workshop on DNA Based Computers, held at the Massachusetts Institute of Technology, Cambridge, MA, USA June 14–15, 1999, American Mathematical Society, 1999, pp. 91-100.

  17. N. P. Gerry, N. E. Witowski, J. Day, R. P. Hammer, G. Barany, and F. Barany, “Universal DNA microarray method for multiplex detection of low abundance point mutations,” Journal of Molecular Biology, vol. 292, pp. 251-262, 1999.

    Article  Google Scholar 

  18. A. J. Hartemink, D. K. Gifford, and J. Khodor, “Automated constraint-based nucleotide sequence selection for DNA computation,” in Proceedings of the 4th DIMACS Workshop on DNA Based Computers, held at the University of Pennsylvania, Philadelphia, 1998, pp. 227-235.

  19. F. Li and G. D. Stormo, “Selection of optimal DNA oligos for gene expression arrays,” Bioinformatics, vol. 17, pp. 1067-1076, 2001.

    Article  Google Scholar 

  20. C. Mao, T. H. LaBean, J. H. Reif, and N. C. Seeman, “Logical computation using algorithmic self-assembly of DNA triple-crossover molecules,” Nature, vol. 407, pp. 493-496, 2000.

    Article  Google Scholar 

  21. A. Marathe, A. E. Condon, and R. M. Corn, “On combinatorial DNA word design,” in Proceedings of the 5th International Meeting on DNA Based Computers, 1999.

  22. C. A. Mirkin, R. L. Letsinger, R. C. Mucic, and J. J. Storhoff, “A DNA-based method for rationally assembling nanoparticles into macroscopic materials,” Nature, vol. 382, pp. 607-609, 1996.

    Article  Google Scholar 

  23. C. M. Niemeyer, “Self-assembled nanostructures based on DNA: towards the development of nanobiotechnology,” Current Opinion in Chemical Biology, vol. 4, pp. 609-618, 2000.

    Article  Google Scholar 

  24. G. Raddatz, M. Dehio, T. F. Meyer, and C. Dehio, “PrimeArray: genome-scale primer design for DNA-microarry construction,” Bioinformatics, vol. 17, pp. 98-99, 2001.

    Article  Google Scholar 

  25. J. A. Rose and R. J. Deaton, “The fidelity of annealing-ligation: A theoretical analysis,” in DNA Computing, 6th International Workshop on DNA-Based Computers, DNA 2000, Leiden, The Netherlands, June 2000, Springer, 2001, pp. 231-246.

  26. J. A. Rose, R. J. Deaton, D. R. Franceschetti, M. Garzon, and S. E. Stevens Jr., “A statistical mechanical treatment of error in the annealing biostep of DNA computation,” in Proceedings of the Genetic and Evolutionary Computation Conference 1999, Morgan Kaufmann, 1999, pp. 1829-1834.

  27. J. A. Rose, R. J. Deaton, M. Hagiya, and A. Suyama, “The fidelity of the tag-antitag system,” in DNA Computing, 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A., 10–13 June 2001, Springer, 2002, pp. 138-149.

  28. A. J. Ruben, S. J. Freeland, and L. F. Landweber, “PUNCH: An evolutionary algorithm for optimizing bit set selection,” in DNA Computing, 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A., 10–13 June 2001, Springer, 2001, pp. 150-160.

  29. W. Rychlik, and R. E. Rhoads, “A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA,” Nucleic Acids Research, vol. 17, pp. 201-209, 1989.

    Google Scholar 

  30. J. SantaLucia Jr., and H. T. Allawi, P. Ananda Seneviratne, “Improved nearest-neighbor parameters for predicting DNA duplex stability,” Biochemistry, vol. 35, pp. 3555-3562, 1996.

    Article  Google Scholar 

  31. N. C. Seeman and N. R. Kallenbach, “Design of immobile nucleic acid junctions,” Biophysical Journal, vol. 44, pp. 201-209, 1983.

    Article  Google Scholar 

  32. N. C. Seeman, “De novo design of sequences for nucleic acid structural engineering,” Journal of Biomolecular Structure & Dynamics, vol. 8, pp. 573-581, 1990.

    Google Scholar 

  33. N. C. Seeman, “DNA engineering and its application to nanotechnology,” Trends in Biotechnology, vol. 17, pp. 437-443, 1999.

    Article  Google Scholar 

  34. S.-Y. Shin, D.-M. Kim, I.-H. Lee, and B.-T. Zhang, “Evolutionary sequence generation for reliable DNA computing,” in Proceedings of the 2002 Congress on Evolutionary Computing CEC'02, 2002, pp. 79-84.

  35. D. D. Shoemaker, R. W. Davis, M. P. Mittmann, and M. S. Morris, “Methods and compositions for selecting tag nucleic acids and probe arrays,” European patent EP0799897, 1997, pp. 79-84.

  36. W. D. Smith, “DNA computers in vitro and in vivo,” in Proceedings of a DIMACS Workshop, held at Princeton University, 4 April 1995, Amer. Math. Soc., 1996, pp. 121-186.

  37. N. Sugimoto, S. Nakano, M. Yoneyama, and K. Honda, “Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes,” Nucleic Acids Research, vol. 24, pp. 4501-4505, 1996.

    Article  Google Scholar 

  38. F. Tanaka, M. Nakatsugawa, M. Yamamoto, T. Shiba, and A. Ohuchi, “Developing Support System for Sequence Design in DNA Computing” in DNA Computing, 7th International Workshop on DNA-Based Computers, DNA 2001, Tampa, U.S.A., 10–13 June 2001, pp. 129-137.

  39. F. Tanaka, M. Nakatsugawa, M. Yamamoto, T. Shiba, and A. Ohuchi, “Towards a general-purpose sequence design system in DNA computing,” in Proceedings of the 2002 Congress on Evolutionary Computing CEC'02, 2002, pp. 73-78.

  40. E. Winfree, X. Yang, and N. C. Seeman, “Universal Computation via Self-assembly of DNA: Some Theory and Experiments” in Proceedings of the 2nd DIMACS Meeting on DNA Based Computers, Princeton University, June 10–12, 1996.

  41. E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman, “Design and self-assembly of two-dimensional DNA crystals,” Nature, vol. 394, pp. 539-544, 1998.

    Article  Google Scholar 

  42. H. Yan, X. Zhang, Z. Shen, and N. C. Seeman, “A robust DNA mechanical device controlled by hybridization topology,” Nature, vol. 415, pp. 62-65, 2002.

    Article  Google Scholar 

  43. B. Yurke, A. J. Turberfield, A. P. Mills Jr., F. C. Simmel, and J. L. Neumann, “A DNA-fuelled molecular machine made of DNA,” Nature, vol. 406, pp. 605-608, 2000.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Chair of Systems Analysis, University of Dortmund, Germany

    Udo Feldkamp & Wolfgang Banzhaf

  2. Informium AG, Cologne, Germany

    Hilmar Rauhe

Authors
  1. Udo Feldkamp
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hilmar Rauhe
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wolfgang Banzhaf
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Feldkamp, U., Rauhe, H. & Banzhaf, W. Software Tools for DNA Sequence Design. Genet Program Evolvable Mach 4, 153–171 (2003). https://doi.org/10.1023/A:1023985029398

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1023985029398

Search

Navigation