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DNA implementation of a Royal Road fitness evaluation

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DNA Computing (DNA 2000)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2054))

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Abstract

A model for DNA implementation of Royal Road evolutionary computations is presented. An encoding for a Royal Road problem is presented. Experimental results utilizing 2-d denaturing gradient gel electrophoresis (2-d DGGE) and polyacrylamide gel electrophoresis (PAGE) for separation by fitness in this sample Royal Road problem are shown. Suggestions for possible use of the MutS and MutY proteins as tools for separation by fitness are given. Plans for future experiments and implementation are discussed.

Supported by NSF Grants No. 9805703 and No. 9980092

Partially supported by NSF Grant No. 9980092 and DARPA/NSF Grant No. 9725021.

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References

  1. Leonard M. Adleman, Computing with DNA, Scientific American 279 (1998), 54–61.

    Article  Google Scholar 

  2. Leonard M. Adleman, Molecular computation of solutions to combinatorial problems, Science 266 (1994), 1021–1024.

    Article  Google Scholar 

  3. K. G. Au, S. Clark, J. H. Miller and P. Modrich, Escherichia coli MutY gene encodes an adenine glycosylase active on G-A mispairs, PNAS 86 (1989), 8877–8881.

    Article  Google Scholar 

  4. Thomas Bäck, David B. Fogel, and Zbigniew Michalewicz, eds., Handbook of Evolutionary Algorithms, Institute of Physics Publishing, Philadelphia, 1997.

    Google Scholar 

  5. Dan Boneh, Christopher Dunworth, and Richard J. Lipton, Breaking DES using a molecular computer, Tech. Report CS-TR-489-95, Princeton University, May 1995.

    Google Scholar 

  6. Alan Dove, From bits to bases: Computing with DNA, Nature Biotechnology 16, no. 9, (1998), 830–832.

    Article  Google Scholar 

  7. I. Biswas and P. Hseih, Identification and Characterization of a Thermostable MutS Homolog from Thermus aquaticus, The Journal of Biological Chemistry 271, (1996), no. 9, 5040–5048.

    Article  Google Scholar 

  8. J. Chen, E. Antipov, B. Lemieux, W. Cedeno, and D.H. Wood, DNA Computing implementing genetic algorithms, Preliminary Proceedings DIMACS Workshop on Evolution as Computation, (L. Landweber, R. Lipton, E. Winfree and S. Freeman, eds), DIMACS, Piscataway, NJ, 1999, 39–49.

    Google Scholar 

  9. David Harlan Wood, Junghuei Chen, Eugene Antipov, Bertrand Lemieux, and Walter Cedeño, In vitro selection for a OneMax DNA evolutionary computation, DNA Based Computers V: DIMACS Workshop, DIMACS series in discrete mathematics and theoretical computer science, June 14–15, 1999, (David Gifford and Erik Winfree, eds.), American Mathematical Society, Providence, to appear.

    Google Scholar 

  10. A. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, and K. Struhl, Current Protocals in Molecular Biology, Greene Publishing Associates and Wiley-Interscience, 1994.

    Google Scholar 

  11. J. C. Cox, P. Rudolph, and A. D. Ellington, Automated RNA selection, Biotechnology Progress 14 (1998), no. 6, 845–850.

    Article  Google Scholar 

  12. S. Fischer and L. Lerman, Proceedings of the National Academy of Science 80 (1983), 1579–1583.

    Article  Google Scholar 

  13. Philippe Gigure and David E. Goldberg, Population sizing for optimum sampling with genetic algorithms: A case study of the Onemax problem, Genetic Programming 1998: Proceedings of the Third Annual Conference at Madison, WI, (John R. Koza, Wolfgang Banzhaf, Kumar Chellapilla, Kalyanmoy Deb, Marco Dorigo, David B. Fogel, Max H. Garzon, David E. Goldberg, Hitoshi Iba, and Rick Riolo, eds), Morgan Kaufman, San Francisco, 1998, 22–25.

    Google Scholar 

  14. Searching for gene defects by denaturing gradient gel electrophoresis, Trends in Biochemical Sciences 172 (1992), no. 3, 89–93.

    Google Scholar 

  15. Jörg Heitkötter and David Beasley, The hitch-hiker’s guide to evolutionary computation, (FAQ for comp.ai.genetic). Web page at http://alife.santafe.edu/joke/encore/www/, September 1999.

  16. A. A. Beaudry and Gerald E. Joyce, Directed evolution of an RNA enzyme, Science 257 (1992), 635–641.

    Article  Google Scholar 

  17. Lila Kari, DNA computing: Arrival of biological mathematics, Math. Intelligencer 19 (1997), no. 2, 9–22.

    Article  MATH  MathSciNet  Google Scholar 

  18. Xianghong Li, Patrick M. Wright and A-Lien Lu, The C-terminal Domain of MutY Glycosylase Determines the 7,8-Dihydro-8-oxo-guanine Specificity and Is Crucial for Mutation Avoidance, The Journal of Biological Chemistry 275 (2000), no. 12, 8448–8455

    Article  Google Scholar 

  19. Richard J. Lipton, DNA solution of hard computational problems, Science 268 (1995), 542–545.

    Article  Google Scholar 

  20. J. R. Lorsch and J. W. Szostak, In vitro evolution of new ribozymes with polynucleotide kinase activity, Nature 371 (1993),31–36.

    Article  Google Scholar 

  21. A Novel Nucleotide Excision Repair for the Conversion of an A/G Mismatch to C/G Base Pair in E. coli, Cell 54 (1988), 805–812.

    Google Scholar 

  22. A-Lien Lu and Ih-Chang Hsu, Detection of Single DNA Base Mutations with Mismatch Repair Enzymes, Genomics 14 (1992), 249–255.

    Article  Google Scholar 

  23. Melanie Mitchell, Stephanie Forrest, and John Holland, The royal road for genetic algorithms: Fitness landscapes and GA performance, Proceedings of the First European Conference on Artificial Life, MIT Press/Bradford Books, Cambridge, MA, 1992.

    Google Scholar 

  24. Melanie Mitchell, An Introduction to Genetic Algorithms,MIT Press, Cambridge, MA,1998.

    MATH  Google Scholar 

  25. Paul Modrich, Mechanisms and Biological Effects of Mismatch Repair, Annu. Rev. Genet. 25 (1991), 229–253.

    Article  Google Scholar 

  26. H. Muir, DNA reveals its talent for computing, New Scientist 144 (1994).

    Google Scholar 

  27. Robert Pool, Forget silicon, try DNA, New Scientist 151 (1996) no. 2038, 26–31.

    Google Scholar 

  28. Erik van Nimwegen, James P. Crutchfield and Melanie Mitchell, Statistical Dynamics of the Royal Road Genetic Algorithm, Theoretical Computer Science, special issue on Evolutionary Computation, to appear (1998).

    Google Scholar 

  29. James P. Crutchfield and Erik van Nimwegen, Optimizing epochal evolutionary search: Population-size independent theory, SFI Working Paper 98-06-046, 1998, 18 pages. Paper found at URL: http://www.santafe.edu/projects/evca/evabstracts.html#oeespsit.

  30. James P. Crutchfield and Erik van Nimwegen, Optimizing epochal evolutionary search: Population-size dependent theory, SFI Working Paper 98-10-090, 1998, 18 pages. Paper found at URL: http://www.santafe.edu/projects/evca/evabstracts.html#oeespsdt.

  31. James P. Crutchfield and Erik van Nimwegen. The evolutionary unfolding of complexity. In Laura Landweber, Erik Winfree, Richard Lipton, and Stephan Freeland, editors, Proceedings of the DIMACS Workshop on Evolution as Computation, New York, 1999, to appear. Springer-Verlag.

    Google Scholar 

  32. M. Sassanfar and J. W. Szostak, An RNA motif that binds ATP, Nature 364 (1993),550–553.

    Article  Google Scholar 

  33. Gerhard Steger, Thermal denaturation of double-stranded nucleic acids: Prediction of termperatures critical for gradient gel electrophoresis and polymerase chain reaction, Nucleic Acids Research 22 (1994), no. 14, 2760–2768.

    Article  Google Scholar 

  34. Willem P.C. Stemmer, DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution, Proceedings of the National Academy of Science, U.S.A. 91 (1994), 389–391.

    Article  Google Scholar 

  35. Willem P.C. Stemmer, The evolution of molecular computation, Science 270 (1995), 1510–1510.

    Article  Google Scholar 

  36. Willem P.C. Stemmer, Sexual PCR and Assembly PCR,The Encyclopedia of Molecular Biology and Molecular Medicine, (Robert Meyers, ed), VCH, New York, 1996, 447–457.

    Google Scholar 

  37. D.H. Wood, J. Chen, E. Antipov, W. Cedeno, and B. Lemieux, A DNA implementation of the Max 1s problem, GECCO-99: Proceedings of the Genetic and Evolutionary Computation Conference, July 1999, Orlando, Florida, (W. Banzhaf, A.E. Eiben, M. Garzon, V. Honavar, M. Jakiela, and R.E. Smith, eds), Morgan Kaufman, San Francisco, 1999, 1835–1842.

    Google Scholar 

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Author information

Authors and Affiliations

  1. University of Delaware, Newark, DE 19716, USA

    Elizabeth Goode, David Harlan Wood & Junghuei Chen

Authors
  1. Elizabeth Goode
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  2. David Harlan Wood
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  3. Junghuei Chen
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of British Columbia, 201-2366 Main Mall, Vancouver, B.C., Canada, V6T 1Z4

    Anne Condon

  2. Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands

    Grzegorz Rozenberg

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© 2001 Springer-Verlag Berlin Heidelberg

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Goode, E., Wood, D.H., Chen, J. (2001). DNA implementation of a Royal Road fitness evaluation. In: Condon, A., Rozenberg, G. (eds) DNA Computing. DNA 2000. Lecture Notes in Computer Science, vol 2054. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44992-2_17

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  • DOI: https://doi.org/10.1007/3-540-44992-2_17

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42076-7

  • Online ISBN: 978-3-540-44992-8

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