Abstract
An integrated scheme based on biochip technology for performing DNA computing is proposed here. This work is motivated by the goal of integrating all the steps of DNA computing into one machine called DNA computing processor. The basic structure of processor consists of making DNA micro-arrays unit, encoding DNA sequences unit, micro-reaction unit, solution extraction unit and micro-control unit. The functions of each unit are discussed in detail, especially for the solution extraction unit, where the optimal solution spaces are extracted. Finally, conclusions are drawn and future studies are discussed.
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References
Adleman, L.M.: Molecular Computation of Solutions to Combinatorial Problems. Science 11, 1021–1023 (1994)
Meng, D.Z., Cao, H.P.: DNA Computing and Biological Mathematics. Acta Biophysica Sinica (in Chinese) 2, 163–174 (2002)
Charlot, B., et al.: Research Activities, http://tima.imag.fr/research/files/gr-04/mns.pdf
Gabig, M., Wegrzyn, G.: An Introduction to DNA Chips: Principles, Technology, Applications and Analysis. Acta Biochimica Polonica 3, 615–622 (2001)
Garzon, M.H., Deaton, R.J.: Codeword Design and Information Encoding in DNA Ensembles. Natural Computing 3, 253–292 (2004)
Tanaka, F., Nakatsugawa, M., Yamamoto, M., Shiba, T., Ohuchi, A.: Developing Support System for Sequence Design in DNA Computing. In: Proc. 7th Int. Workshop DNA Based Comput., pp. 340–349 (2001)
Frutos, A.G., et al.: Demonstration of a Word Design Strategy for DNA Computing on Surfaces. Nucleic Acids Res. 23, 4748–4757 (1997)
Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular Computation: RNA Solutions to Chess Problems. Proc. Natl. Acad. Sci. U.S.A. 97, 1385–1389 (2000)
Arita, M., Kobayashi, S.: DNA Sequence Design Using Templates. New Generation Comput. 20, 263–277 (2002)
Arita, M., et al.: Improving Sequence Design for DNA Computing. In: Proc. Genetic Evol. Comput., pp. 875–882 (2000)
Tuplan, D.C., Hoose, H., Condon, A.: Stochastic Local Search Algorithms for DNA Word Design. In: Proc. 8th Int. Workshop DNA Based Comput., pp. 229–241 (2002)
Andronescu, M., et al.: Algorithms for Testing that DNA Word Designs Avoid Unwanted Secondary Structure. In: Proc. 8th Int. Workshop DNA Based Comput., pp. 182–195 (2002)
Zhang, B.T., Shin, S.Y.: Molecular Algorithms for Efficient and Reliable DNA Computing. In: Proc. Genetic Program (GP), pp. 735–742 (1998)
Feldkamp, U., Saghafi, S., Banzhaf, W., Rauhe, H.: DNA Sequence Generator–A Program for the Construction of DNA Sequences. In: Proc.7th Int. Workshop DNA Based Comput., pp. 179–188 (2001)
Hartemink, A.J., Gifford, D.K., Khodor, J.: Automated Constraint Based Nucleotide Sequence Selection for DNA Computation. In: Proc. 4th DIMACS Workshop DNA Based Comput., pp. 227–235 (1998)
Deaton, R., Chen, J., Bi, H., Rose, J.A.: A Software Tool for Generating Noncrosshybridization Libraries of DNA Oligonucleotides. In: Proc. 8th Int. Workshop DNA Based Comput., pp. 252–261 (2002)
Deaton, R., et al.: A PCR-Based Protocol for in Vitro Selection of Noncrosshybridizing Olgionucleotides. In: Proc. 8th Int. Workshop DNA Based Comput., pp. 196–204 (2002)
Tanaka, F., Kameda, A., Yamamoto, M., Ohuchi, A.: Design of Nucleic Acid Sequences for DNA Computing Based on a Thermodynamic Approach. Nucleic Acids Res. 3, 903–911 (2005)
Shin, S.Y., Lee, I.H., Kim, D., Zhang, B.T.: Multi-Objective Evolutionary Optimization of DNA Sequences for Reliable DNA Computing. IEEE Trans. Evol. Comput. 2, 143–158 (2005)
Taylor, T.B., Emily, S., et al.: Optimization of the Performance of the Polymerase Chain Reaction in Silicon-Based Microstructures. Nucleic Acids Res. 15, 3164–3168 (1997)
Braich, R.S., Chelyapov, N., et al.: Solution of a 20-Variable 3-SAT Problem on a DNA Computer. Science 19, 499–502 (2002)
Liu, Q.H., Wang, L., et al.: DNA Computing on Surfaces. Nature 13, 175–178 (2000)
Zhang, F.Y., Yin, Z.X., et al.: DNA Computation Model to Solve 0-1 Programming Problem. Biosystems 74, 9–14 (2004)
Shi, X.L., Li, X., Zhang, Z., et al.: Improce Capability of DNA Automaton: DNA Automaton with three Internal States and Tape Head Move in Two Directions. In: Huang, D.-S., Zhang, X.-P., Huang, G.-B. (eds.) ICIC 2005. LNCS, vol. 3645, pp. 71–79. Springer, Heidelberg (2005)
Wang, H., Lin, B.C.: Capillary Electrophoresis on Microchip and its Application in Life Science. Journal of Analytical Chemistry (in Chinese) 3, 359–364 (2002)
Thompson, S.: Chemiluminescent Detection of Nucleic Acids. International Biotechnology Laboratory 10, 14 (2000)
Momoko, K., Tamao, O., et al.: Laser-Induced Fluorescence Microscopic System Using an Optical Parametric Oscillator for Tunable Detection in Microchip Analysis. Analytical and Bioanalytical Chemistry 4, 992–995 (2005)
Scott, E., Van, B.: An Introduction to Mass Spectrometry, http://science.widener.edu/svb/massspec/massspec.pdf
Walter, R., Vandaveer, S.A., et al.: Recent Developments in Electrochemical Detection for Microchip Capillary Electrophoresis. Electrophoresis 25, 3528–3549 (2004)
Ennis, M.A., Gelfand, D.H., et al.: PCR Protocols: a Guide to Methods and Applications. Academic Press, Inc., London (1990)
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Wang, YF., Cui, GZ., Huang, BY., Pan, LQ., Zhang, XC. (2006). DNA Computing Processor: An Integrated Scheme Based on Biochip Technology for Performing DNA Computing. In: Huang, DS., Li, K., Irwin, G.W. (eds) Computational Intelligence and Bioinformatics. ICIC 2006. Lecture Notes in Computer Science(), vol 4115. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11816102_27
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DOI: https://doi.org/10.1007/11816102_27
Publisher Name: Springer, Berlin, Heidelberg
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