Abstract
In the last decade, the implementation of computations using DNA has attracted a lot of attention from both computer scientists and biologists. Molecular computation has many advantages, including small size, a biological interface and massive parallelism. This potential offers interesting possibilities for the implementation of evolutionary computation using DNA. We discuss the potential of evolutionary DNA computing and experimental progress.
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Păun, G., Rozenberg, G., Salomaa, A.: DNA Computing: New Computing Paradigms. Springer, Heidelberg (1998)
Adleman, L.M.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1024 (1994)
Schneider, T.D.: Theory of Molecular Machines. II. Energy Dissipation from Molecular Machines. J. Theor. Biol. 148, 125–137 (1991)
Ouyang, Q., Kaplan, P.D., Liu, S.M., Libchaber, A.: DNA Solution of the Maximal Clique Problem. Science 278, 446–449 (1997)
Yoshida, H., Suyama, A.: Solution to 3-SAT by Breadth First Search. In: WInfree, E., Gifford, D.K. (eds.) DNA Based Computers V, pp. 9–22. American Mathematical Society, Providence, RI (2000)
Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular Computation: RNA Solutions to Chess Problems. Proc. Natl. Acad. Sci. USA 91, 1385–1389 (2000)
Head, T., Rozenberg, G., Bladergroen, R.S., Breek, C.K.D., Lommerse, P.H.M., Spaink, H.P.: Computing with DNA by Operating on Plasmids. Biosystems 57, 87–93 (2000)
Liu, Q., Wang, L., Frutos, A.G., Condon, A.E., Corn, R.M., Smith, L.M.: DNA Computing on Surfaces. Nature 403, 175–179 (2000)
Sakamoto, K., Gouzu, H., Komiya, K., Kiga, D., Yokoyama, S., Yokomore, T., Hagiya, M.: Molecular Computation by DNA Hairpin Formation. Science 288, 1223–1226 (2000)
Wang, L., Hall, J.G., Lu, M., Liu, Q., Smith, L.M.: A DNA Computing Readout Operation Based on Structure-Specific Cleavage. Nat. Biotechnol. 19, 1053–1059 (2001)
Braich, R.S., Chelyapov, N., Johnson, C., Rothemund, P.W.K., Adleman, L.: Solution to a 20-Variable 3-SAT Problem on a DNA Computer. Science 296, 499–502 (2002)
Schmidt, K.A., Henkel, C.V., Rozenberg, G., Spaink, H.P.: DNA Computing Using Single-Molecule Hybridization Detection. Nucleic Acids Res. 32, 4962–4968 (2004)
Ogihara, M., Ray, A.: DNA-Based Parallel Computing by ’Counting’. In: Rubin, H., Wood, D.H. (eds.) DNA Based Computers III: DIMACS Workshop, pp. 265–274. American Mathematical Society, Providence, RI (1997)
Lipton, R.J.: DNA Solution of Hard Computational Problems. Science 268, 542–545 (1995)
Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N.V., Goodman, M.F., Adleman, L.M., Rothemund, P.W.K.: A Sticker-Based Model for DNA Computation. J. Comput. BIol. 5, 615–629 (1998)
Rozenberg, G., Spaink, H.: DNA Computing by Blocking. Theor. Comput. Sci. 292, 653–665 (2003)
Henkel, C.V.: Experimental DNA Computing. PhD thesis, Leiden University (2005)
Mauri, G., Ferretti, C.: Word Design for Molecular Computing: a Survey. In: Chen, J., Reif, J. (eds.) DNA Computing, 9th International Workshop on DNA Based Computers, pp. 37–47. Springer, Heidelberg (2004)
Heldkamp, U., Rauhe, H., Banzhaf, W.: Software Tools for DNA Sequence Design. Genetic Programming and Evolvable Machines 4, 153–171 (2003)
Hagiya, M.: From Molecular Computing to Molecular Programming. In: Condon, A., Rozenberg, G. (eds.) DNA Computing, 6th International Workshop on DNA-Based Computers, pp. 89–102. Springer, Heidelberg (2001)
Gehani, A., Reif, J.: Micro Flow Bio-Molecular Computation. Biosystems 52, 197–216 (1999)
McCaskill, J.S.: Optically Programming DNA Computing in Microflow Reactors. Biosystems 59, 125–138 (2001)
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)
Stemmer, W.P.C.: The Evolution of Molecular Computation. Science 270, 1510 (1995)
Adleman, L.M.: On Constructing a Molecular Computer. In: Lipton, R.J., Baum, E. (eds.) DNA Based Computers, DIMACS 27, pp. 1–21. American Mathematical Society, Providence, RI (1996)
Deaton, R., Murphy, R.C., Rose, J.A., Garzon, M., Franschetti, D.R., Stevens Jr., S.E.: A DNA Based Implementation of an Evolutionary Search for Good Encodings for DNA Computation. In: Proceedings of the Fourth IEEE Conference on Evolutionary Computation, Indianapolis, IN, pp. 267–271. IEEE Press, Piscataway (1997)
Chen, J., Wood, D.H.: Computation with Biomolecules. Proc. Natl. Acad. Sci. USA 97, 1328–1330 (2000)
Bäck, T., Kok, J.N., Rozenberg, G.: Evolutionary Computation as a Paradigm for DNA-Based Computation. In: Landweber, L.F., Winfree, E. (eds.) Evolution as Computation. DIMACS Workshop, Princeton, pp. 15–40. Springer, Heidelberg (2003)
Nuser, M., Deaton, R.: Simulations of DNA Computing with In Vitro Selection. Genetic Programming and Evolvable Machines 4, 173–183 (2003)
Stemmer, W.P.C.: Rapid Evolution of a Protein In Vitro by DNA Shuffling. Nature 370, 389–391 (1994)
Minshull, J., Stemmer, W.P.C.: Protein Evolution by Molecular Breeding. Curr. Opin. Chem. Biol. 3, 284–290 (1999)
Joyce, G.F.: Directed Evolution of Nucleic Acid Enzymes. Annu. Rev. Biochem. 73, 791–836 (2004)
Nataraj, A.J., Olivos-Glander, I., Kusukawa, N., Highsmith, W.E.: Single-Strand Conformation Polymorphism an Heteroduplex Analysis for Gel-Based Mutation Detection. Electrophoresis 20, 1177–1185 (1999)
Wood, D., Chen, J., Antipov, E., Lemieux, B., Cedeno, W.: A DNA Implementation of the Max 1s Problem. In: Banzhaf, W., Eiben, A.E., Garzon, M.H., Honavar, V., Jakiela, M., Smith, R.E. (eds.) Proceedings of the Genetic and Evolutionary Computation Conference 1999, pp. 1835–1841. Morgan Kaufman, San Francisco (1999)
Goode, E., Wood, D.H., Chen, J.: DNA Implementation of a Royal Road Fitness Evaluation. In: Condon, A., Rozenberg, G. (eds.) DNA Computing, Proceedings 6th International Workshop on DNA-Based Computers, pp. 247–262. Springer, Heidelberg (2001)
Henkel, C.V., Rozenberg, G., Spaink, H.P.: Application of Mismatch Detection Methods in DNA Computing. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA10, Tenth International Meeting on DNA Computing, Preliminary Proceedings, Università di Milano-Bicocca, pp. 183–192 (2004)
Loakes, D.: The Application of Universal DNA Base Analogues. Nucleic Acids Res. 29, 2437–2447 (2001)
Gottlieb, J., Marchiori, E., Rossi, C.: Evolutionary Algorithms for the Satisfiability Problem. Evol. Comput. 10, 35–50 (2002)
Upchurch, D.A., Shankarappa, R., Mullins, J.I.: Position and Degree of Mismatches and the Mobility of DNA Heteroduplexes. Nucleic Acids Res. 69, e69 (2000)
Fraenkel, A.S.: Protein Folding, Spin Glass and Computational Complexity. In: Rubin, H., Wood, D.H. (eds.) DNA Based Computers III, Proceedings DIMACS Workshop, pp. 101–121. American Mathematical Society, Providence (1999)
Pierce, N.A., Winfree, E.: Protein Design is NP-Hard. Protein Eng. 15, 779–782 (2002)
Deaton, R., Chen, J., Bi, H., Rubin, H., Wood, D.H.: A PCR-Based Protocol for In Vitro Selection of Non-Crosshybridizing Oligonucleotides. In: Hagiya, M., Ohuchi, A. (eds.) DNA Computing, 8th International Workshop on DNA-Based Computers, pp. 196–204. Springer, Heidelberg (2003)
Chen, J., Deaton, R., Garzon, M., Kim, J.W., Wood, D., Bi, H., Carpenter, D., Wang, Y.Z.: Characterization of Non-Crosshybridizing DNA Oligonucleotides Manufactured In Vitro. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA10, Tenth International Meeting on DNA Computing, Preliminary Proceedings, Università di Milano-Bicocca, pp. 132–141 (2004)
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Henkel, C.V., Kok, J.N. (2005). Towards Evolutionary DNA Computing. In: Mira, J., Álvarez, J.R. (eds) Mechanisms, Symbols, and Models Underlying Cognition. IWINAC 2005. Lecture Notes in Computer Science, vol 3561. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11499220_26
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DOI: https://doi.org/10.1007/11499220_26
Publisher Name: Springer, Berlin, Heidelberg
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