Summary
According to the author’s view, research in the field of DNA and molecular computing is expanding into broader applications in nanotechnology and biotechnology, and the principles and methods for designing molecular systems with information-processing capability for such applications are considered important. We call research into designing such molecular systems molecular programming. This chapter first summarizes a recent international conference in this field, DNA8, the Eighth International Meeting on DNA Based Computers, to support the above, rather personal view on the field. Next, it reviews existing models of DNA and molecular computation and analyses the results of these models, and then briefly describes some methods for molecular programming, including sequence design. It finally touches on molecular machines made of DNA, one of the current focuses of molecular programming.
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References
Adleman, L.M.: Molecular computation of solutions to combinatorial problems, Science 266, 1021–1024 (1994).
Andronescu, M., Dees, D., Slaybaugh, L., Zhao, Y., Condon, A.E., Cohen, B., Skiena, S.: Algorithms for testing that DNA word designs avoid unwanted secondary structure. In: Proceedings of the Eighth International Meeting on DNA Based Computers (2003) 92–104.
Arita, M., Kobayashi, S.: DNA sequence design using templates, New Generation Computing 20, 263–277 (2002).
Basu, S., Karig, D., Weiss, R.: Engineering signal processing in cells: Towards molecular concentration band detection. In: Proceedings of the Eighth International Meeting on DNA Based Computers (2003) 80–89.
Beaver, D.: A universal molecular computer. In: DNA Based Computers. DIMACS Series in Discrete Mathematics and Theoretical Computer Science vol.27 (1996) 29–36.
Benenson, Y., Paz-Elizur, T., Adar, R., Heina, E., Livneh, Z., Shapiro, E.: Programmable and autonomous computing machine made of biomolecules, Nature 414, 430–434 (2001).
Cantor, C.R., Schimmel, P.R.: Biophysical Chemistry, Part III: The behavior of biological macromolecules (W.H. Freeman, San Francisco 1980).
Flamm, C., Hofacker, I.L., Maurer-Stroh, S., Stadler, P.F., Zehl, M.: Design of multistable RNA molecules, RNA 7, 254–265 (2001).
Frutos, A.G., Liu, Q., Thiel, A.J., Sanner, A.M.W., Condon, A.E., Smith, L.M., Corn, R.M.: Demonstration of a word design strategy for DNA computing on surfaces, Nucleic Acids Research 25(23), 4748–4757 (1997).
Garzon, M., Neathery, P., Deaton, R.J., Murphy, R.C., Franceschetti, D.R., Stevens, S.E. Jr.: A new metric for DNA computing. In: Proceedings of 2nd Annual Genetic Programming Conference (1997) 472–478.
Hagiya, M.: Perspectives on molecular computing, New Generation Computing 17(2), 131–140 (1999).
Hagiya, M.: From molecular computing to molecular programming. In DNA Computing, 6th International Workshop on DNA Based Computers, DNA 2000. Lecture Notes in Computer Science, vol 2054 (Springer, Berlin Heidelberg New York (2001) 89–102.
Hagiya, M., Arita, M., Kiga, D., Sakamoto, K., Yokoyama, S.: Towards parallel evaluation and learning of Boolean μ-formulas with molecules. In: DNA Based Computers III. DIMACS Series in Discrete Mathematics and Theoretical Computer Science vol.48 (1999) 57–72.
Hagiya, M., Ohuchi, A. (Eds.): Proceedings of the Eighth International Meeting on DNA Based Computers. Lecture Notes in Computer Science, vol.2568 (Springer, Berlin Heidelberg New York dy2003).
Heitsch, C.E., Condon, A.E., Hoos, H.H.: From RNA secondary structure to coding theory: A combinatorial approach. In: Proceedings of the Eighth International Meeting on DNA Based Computers (2003) 125–136.
Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M., Schuster, P.: Fast folding and comparison of RNA secondary structures, Monatshefte Chem. 125, 167–188 (1994).
Karp, R., Kenyon, C., Waarts, O.: Error-resilient DNA computations. In: Seventh ACM-SIAM Symposium on Discrete Algorithms (1996) 458–467.
Kobayashi, S., Kondo, T., Arita, M.: On template method for DNA sequence design. In: Proceedings of the Eighth International Meeting on DNA Based Computers (2003) 115–124.
Komiya, K., Sakamoto, K., Gouzu, H., Yokoyama, S., Arita, M., Nishikawa, A., Hagiya, M.: Successive state transitions with I/O interface by molecules. In: DNA Computing, 6th International Meeting on DNA Based Computers, DNA 2000. Lecture Notes in Computer Science, vol.2054 (Springer, Berlin Heidelberg New York 2001) 17–26.
Kurtz, S.A., Mahaney, S.R., Royer, J.S., Simon, J.: Active transport in biological computing. In: DNA Based Computers II. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol.44 (1999) 171–179.
Lipton, R.J.: DNA solution of hard computational problems, Science 268, 542–545 (1995).
Mao, C., Sun, W., Shen, Z., Seeman, N.C.: A nanomechanical device based on the B-Z transition of DNA, Nature 397, 144–146 (1999).
McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure, Biopolymers 29, 1105–1119 (1990).
Nishikawa, A., Yamamura, M., Hagiya, M.: DNA computation simulator based on abstract bases, Soft Computing 5(1), 25–38 (2001).
Ogihara, M., Ray, A.: DNA based self-propagating algorithm for solving bounded-fan-in Boolean circuits. In: Genetic Programming’ 98 (1998) 725–730.
Ogihara, M., Ray, A.: DNA Based parallel computation by “counting”. In: DNA Based Computers III. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol.48 (1999) 255–264.
Păun, G.: Membrane Computing — An Introduction (Springer, Berlin Heidelberg New York 2002).
Păun, G., Rozenberg, G., Salomaa, A.: DNA Computing (Springer, Berlin Heidelberg New York 1998).
Reif, J.H.: Parallel molecular computation. In: Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (1995) 213–223.
Rooß, D., Wagner, K.W.: On the power of DNA-computing, Information and Computation 131, 95–109 (1996).
Rose, J.A., Hagiya, M., Deaton, R.J., Suyama, A.: A DNA based in vitro genetic program, Journal of Biological Physics 28, (2003).
Rothemund, P.W.K., Winfree, E.: The program-size complexity of selfassembled squares. In: Proceedings of the Thirty-Second Annual ACM Symposium on Theory of Computing (2000) 459–468.
Roweis, S., Winfree, E., Burgoyne, R, Chelyapov, N.V., Goodman, M.F., Rothemund, P.W.K., Adleman, L.M.: A sticker based model for DNA computation. In: DNA Based Computers II. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol.44 (1999) 1–29.
Sakakibara, Y., Suyama, A.: Intelligent DNA chips: Logical operation of gene expression profiles on DNA computers. In: Genome Informatics 2000. Genome Informatics Series, vol.11 (Universal Academy Press, Tokyo 2000) 33–42.
Sakamoto, K., Gouzu, H., Komiya, K., Kiga, D., Yokoyama, S., Yokomori, T., Hagiya, M.: Molecular computation by DNA hairpin formation, Science 288, 1223–1226 (2000).
Sakamoto, K., Kiga, D., Komiya, K., Gouzu, H., Yokoyama, S., Ikeda, S., Sugiyama, H., Hagiya, M.: State transitions by molecules, BioSystems 52, 81–91 (1999).
SantaLucia, J. Jr., Allawi, H.T., Seneviratne, P.A.: Improved nearest-neighbor parameters for predicting DNA duplex stability, Biochemistry 35(11), 3555–3562 (1996).
Schuler, G.D.: Electronic PCR: Bridging the gap between genome mapping and genome sequencing, Trends in Biotechnology 16(11), 456–459 (1998).
Seeman, N.C., et al: The perils of polynucleotides: The experimental gap between the design and assembly of unusual DNA structures. In: DNA Based Computers II. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol 44 (1999) 215–233.
Suyama, A., Nishida, N., Kurata, K., Omagari, K.: Gene expression analysis by DNA computing. In: Currents in Computational Molecular Biology (2000) 12–13.
Weiss, R., Knight, T.F. Jr.: Engineered communications for microbial robotics. In: DNA Computing, 6th International Meeting on DNA Based Computers DNA 2000. Lecture Notes in Computer Science, vol.2054 (Springer, Berlin Heidelberg New York 2001) 1–16.
Winfree, E.: Simulations of computing by self-assembly. In: Preliminary Proceedings, Fourth International Meeting on DNA Based Computers, 1998 (University of Pennsylvania) 213–239. Also in Erik Winfree’s PhD Thesis: Algorithmic Self-Assembly of DNA (California Institute of Technology, 1998).
Winfree, E., Eng, T., Rozenberg, G.: String tile models for DNA computing by self-assembly. In: DNA Computing, 6th International Meeting on DNA Based Computers, DNA 2000. Lecture Notes in Computer Science, vol.bd2054 (Springer, Berlin Heidelberg New York 2001) 63–88.
Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals, Nature 394, 539–544 (1998).
Winfree, E., Yang, X., Seeman, N.C.: Universal computation via self-assembly of DNA: some theory and experiments. In: DNA Based Computers II. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol.44 (1999) 191–213.
Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: A robust DNA mechanical device controlled by hybridization topology, Nature 415, 62–65 (2002).
Yoshida, H., Suyama, A.: Solutions to 3-SAT by breadth first search. In: DNA Based Computers V. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol.54 (1999) 9–22.
Yurke, B., Turberfield, A.J., Mills, A.P. Jr., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA, Nature 406, 605–608 (2000).
Zuker, M., Steigler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Research 9, 133–148 (1981).
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Hagiya, M. (2004). Towards Molecular Programming — a Personal Report on DNA8 and Molecular Computing. In: Ciobanu, G., Rozenberg, G. (eds) Modelling in Molecular Biology. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18734-6_6
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DOI: https://doi.org/10.1007/978-3-642-18734-6_6
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