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Improving Initial Pool Generation of Direct-Proportional Length-Based DNA Computing by Parallel Overlap Assembly

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Soft Computing as Transdisciplinary Science and Technology

Part of the book series: Advances in Soft Computing ((AINSC,volume 29))

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Abstract

A direct-proportional length-based DNA computing approach for weighted graph problems has been proposed where the cost of each path is encoded by the length of oligonucleotides in a proportional way. During the initial pool generation, the hybridization/ligation phase is carried out where all the combinations are generated in the solution. However, this encoding suffers from biological behavior of hybridization since longer oligonucleotides are more likely to hybridize as oppose to the shorter ones. Recently, parallel overlap assembly (POA) has been recognized as an efficient initial pool generation of DNA computing for weighted graph problems. If POA is employed during the initial pool generation of direct-proportional length-based DNA computing, we expected that the biological influence contributed by various lengths of the oligonucleotides could be minimized as much as possible. Thus, in this paper we found that the hybridization/ligation method should be replaced with parallel overlap assembly, for a better and efficient initial pool generation of direct-proportional length-based DNA computing.

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References

  1. Adleman, L.: Molecular Computation of Solutions to Combinatorial Problems. Science, Vol. 266 (1994) 1021–1024

    Article  Google Scholar 

  2. 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. Preliminary Proceeding of the 10th International Meeting on DNA Computing (2004) 357–364

    Google Scholar 

  3. Kaplan, P.D., Ouyang, Q., Thaler, D.S., Libchaber, A.: Parallel Overlap Assembly for the Construction of Computational DNA Libraries. Journal of Theoretical Biology, Vol. 188, Issue 3 (1997) 333–341

    Article  Google Scholar 

  4. 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, Vol. 77 (1989) 51–59

    Article  Google Scholar 

  5. 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., Vol. 88 (1991) 4084–4088

    Article  Google Scholar 

  6. 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, Vol. 164 (1995) 49–53

    Article  Google Scholar 

  7. DeSalle, R., Barcia, M., Wray, C.: PCR Jumping in Clones of 30-million-year-old DNA Fragments from Amber Preserved Termites. Experientia, Vol. 49 (1993) 906–909

    Article  Google Scholar 

  8. Stemmer, W.P.: DNA Shuffling by Random Fragmentation and Reassembly: In Vitro Recombination for Molecular Evolution. Proc. Natl. Acad. Sci. U.S.A., Vol. 91 (1994) 10747

    Article  Google Scholar 

  9. 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., Vol. 98 (2000) 1385–1389

    Article  Google Scholar 

  10. Braich, R.S., Chelyapov, N., Johnson, C., Rothermund, P.W.K., Adleman, L. Solution of a 20-variable 3-SAT Problem on a DNA Computer. Science, Vol. 296 (2002) 499–502

    Article  Google Scholar 

  11. 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, Vol. 1, Issue 1 (2004) 46–60

    Google Scholar 

  12. Udo, F., Sam, S., Wolfgang, B., Hilmar, R.: DNASequenceGenerator: A Program for the Construction of DNA Sequences. Proceedings of the Seventh International Workshop on DNA Based Computers (2001) 23–32

    Google Scholar 

  13. Narayanan, A., Zorbalas, S.: DNA Algorithms for Computing Shortest Paths. Proceedings of Genetic Programming (1998) 718–723

    Google Scholar 

  14. Yamamoto, Y., Kameda, A., Matsuura, N., Shiba, T., Kawazoe, Y., Ahochi, A.: Local Search by Concentration-Controlled DNA Computing. International Journal of Computational Intelligence and Applications, Vol. 2 (2002) 447–455

    Article  Google Scholar 

  15. 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. Lecture Notes in Computer Science, Vol. 2568 (2003) 73–84

    Google Scholar 

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Author information

Authors and Affiliations

  1. Institute of Applied DNA Computing, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki-shi, Kanagawa-ken, 214-8571, Japan

    Zuwairie Ibrahim, Yusei Tsuboi & Osamu Ono

  2. Center for Artificial Intelligence and Robotics (CAIRO), Universiti Teknologi Malaysia, Jalan Semarak, 54100, Kuala Lumpur, Malaysia

    Marzuki Khalid

Authors
  1. Zuwairie Ibrahim
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  2. Yusei Tsuboi
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  3. Osamu Ono
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  4. Marzuki Khalid
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Editor information

Editors and Affiliations

  1. Dept. of Computer Science, Oklahoma State University, North Greenwood Avenue 700, 74106, Tulsa, USA

    Ajith Abraham

  2. Dept. of Computer Science and Systems Engineering, Muroran Institute of Technology, Mizumoto-cho 27-1, 050-8585, Muroran, Hokkaido, Japan

    Yasuhiko Dote

  3. Dept. of Computational Science and Engineering, Nagoya University, Furo-cho, Chikusa-ku, 464-8601, Nagoya, Aichi-ken, Japan

    Takeshi Furuhashi

  4. Institut für Sicherheits-/Prüftechnik, Fraunhofer IPK Berlin, Pascalstr. 8-9, 10587, Berlin, Germany

    Mario Köppen

  5. Division of Complex Systems Technology Graduate School of Engineering, University of Hokkaido, N-13, W-8 060 KITA-KU, Sapporo, Japan

    Azuma Ohuchi

  6. PRESTO Japan Science & Technology Corp. GSSM, University of Tsukuba, 3-29-1 Otsuka, Bunkyo-ku, 12-0012, Tokyo, Japan

    Yukio Ohsawa

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© 2005 Springer-Verlag Berlin Heidelberg

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Ibrahim, Z., Tsuboi, Y., Ono, O., Khalid, M. (2005). Improving Initial Pool Generation of Direct-Proportional Length-Based DNA Computing by Parallel Overlap Assembly. In: Abraham, A., Dote, Y., Furuhashi, T., Köppen, M., Ohuchi, A., Ohsawa, Y. (eds) Soft Computing as Transdisciplinary Science and Technology. Advances in Soft Computing, vol 29. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-32391-0_42

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  • DOI: https://doi.org/10.1007/3-540-32391-0_42

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25055-5

  • Online ISBN: 978-3-540-32391-4

  • eBook Packages: EngineeringEngineering (R0)

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