Abstract
DNA computing often makes use of hybridization, whether for vastly generating the initial candidate answers or amplification by using polymerase chain reaction (PCR). The main idea behind DNA computing approaches for solving weighted graph problems is that if the degree of hybridization can be controlled, then it is able to generate more double stranded DNAs (dsDNAs), which represent the answer of the problem during in vitro computation. Previously, length, concentration, and melting temperature, have been exploited for encoding of weights of a weighted graph problem. In this paper, we present a hybrid approach, which is called concentration-controlled direct-proportional length-based DNA computing (CCDPLB-DNAC), that combines two characteristics: length and concentration, for encoding and at the same time, effectively control the degree of hybridization of DNA. The encoding by length is realized whereby the cost of each path is encoded by the length of the oligonucleotides (oligos) in a proportional way. On the other hand, the hybridization control by concentration is done by varying the amount of oligos, as the input of computation, before the computation begins. The advantage is such that, after an initial pool generation and amplification, polyacrylamide gel electrophoresis (PAGE) can be performed to separate the survived dsDNAs according to their length, which directly decodes the results. The proposed approach shows significant improvement in term of materials used and scalability. The experimental results show the effectiveness of the proposed CCDPLB-DNAC for solving weighted graph problems, such as the shortest path problem.
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References
Adleman, L.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1024 (1994)
Narayanan, A., Zorbalas, S.: DNA Algorithms for Computing Shortest Paths. In: Proceedings of Genetic Programming, pp. 718–723 (1998)
Lee, J.Y., Shin, S.Y., Augh, S.J., Park, T.H., Zhang, B.T.: Temperature Gradient-Based DNA Computing for Graph Problems with Weighted Edges. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 73–84. Springer, Heidelberg (2003)
Ibrahim, Z., Tsuboi, Y., Ono, O., Khalid, M.: Direct-Proportional Length-Based DNA Computing for Shortest Path Problem. International Journal of Computer Science and Applications (IJCSA), Technomathematics Research Foundation 1, 46–60 (2004)
Yamamoto, M., Kameda, A., Matsuura, N., Shiba, T., Kawazoe, Y., Ahochi, A.: A Separation Method for DNA Computing Based on Concentration Control. New Generation Computing 20, 251–262 (2002)
Lee, J.Y., Shin, S.Y., Augh, S.J., Park, T.H., Zhang, B.T.: Temperature Gradient-Based DNA Computing for Graph Problems with Weighted Edges. In: Preliminary Proceedings of the Eighth International Meeting on DNA Based Computers, pp. 41–50 (2002)
Yamamoto, M., Matsuura, N., Shiba, T., Ohuchi, A.: DNA Solution of the Shortest Path Problem by Concentration Control. Genome Informatics, 466–467 (2000)
Udo, F., Sam, S., Wolfgang, B., Hilmar, R.: DNA Sequence Generator: A Program for the Construction of DNA Sequences. In: Proceedings of the Seventh International Workshop on DNA Based Computers, pp. 23–32 (2001)
Sugimoto, N., Nakano, S., Yoneyama, M., Honda, K.: Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes. Nucleic Acid Research 24, 4501–4505 (1996)
Lee, J.Y., Lim, H.W., Yoo, S.I., Zhang, B.T., Park, T.H.: Efficient Initial Pool Generation for Weighted Graph Problems using Parallel Overlap Assembly. In: Preliminary Proceedings of the Tenth International Meeting on DNA Based Computers, pp. 357–364 (2004)
Kaplan, P.D., Ouyang, Q., Thaler, D.S., Libchaber, A.: Parallel Overlap Assembly for the Construction of Computational DNA Libraries. Journal of Theoretical Biology 188(3), 333–341 (1997)
Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K., Pease, L.R.: Site-Directed Mutagenesis by Overlap Extension using the Polymerase Chain Reaction. Gene 77, 51–59 (1989)
Jayaraman, K., Fingar, S.A., Fyles, J.: Polymerase Chain Reaction-Mediated Gene Synthesis: Synthesis of a Gene Coding for Isozymec of Horseradish Peroxidase. Proc. Natl. Acad. Sci. U.S.A. 88, 4084–4088 (1991)
Stemmer, W.P., Crameri, A., Ha, K.D., Brennan, T.M., Heyneker, H.L.: Single-Step Assembly of a Gene and Entire Plasmid from Large Numbers of Oligodeoxyribonucleotides. Gene 164, 49–53 (1995)
DeSalle, R., Barcia, M., Wray, C.: PCR Jumping in Clones of 30-million-year-old DNA Fragments from Amber Preserved Termites. Experientia 49, 906–909 (1993)
Stemmer, W.P.: DNA Shuffling by Random Fragmentation and Reassembly: In Vitro Re-combination for Molecular Evolution. Proc. Natl. Acad. Sci. U.S.A. 91, 10747 (1994)
Zucca, M.: DNA Based Computational Models: Ph.D. Thesis, Politecnico di Torino, Italy (2000)
Noort, D., Gast, F.U., McCaskill, J.S.: DNA Computing in Microreactors. In: Jonoska, N., Seeman, N.C. (eds.) DNA 2001. LNCS, vol. 2340, pp. 33–45. Springer, Heidelberg (2002)
Ibrahim, Z., Tsuboi, T., Ono, O., Khalid, M.: A Study on Lower Bound of Direct-Proportional Length-Based DNA Computing for Shortest Path Problem. In: Zhang, J., He, J.-H., Fu, Y. (eds.) CIS 2004. LNCS, vol. 3314, pp. 71–76. Springer, Heidelberg (2004)
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Ibrahim, Z., Tsuboi, Y., Ono, O., Khalid, M. (2006). Hybrid Concentration-Controlled Direct-Proportional Length-Based DNA Computing for Numerical Optimization of the Shortest Path Problem. In: Ijspeert, A.J., Masuzawa, T., Kusumoto, S. (eds) Biologically Inspired Approaches to Advanced Information Technology. BioADIT 2006. Lecture Notes in Computer Science, vol 3853. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11613022_18
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DOI: https://doi.org/10.1007/11613022_18
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