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Cascading Whiplash PCR with a Nicking Enzyme

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DNA Computing (DNA 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2568))

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Abstract

Whiplash PCR has been proposed as a unique mechanism realizing autonomous inference machines and used in various applications of DNA coumputing. However, it is not easy to increase step sizes within a single molecule because of back annealing. This paper proposes a sheme to cascade results of WPCR from molecules to molecules by using a nicking enzyme. We also show preliminary experiments to produce output fragments continuously from WPCR.

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References

  1. M. Hagiya, M. Arita, D. Kiga, K. Sakamoto, and S. Yokoyama, “Towards parallel evaluation of Boolean μ-formulas with molecules”, in (H. Rubin and D.H. Wood,Eds.) DNA Based ComputersIII, (American Mathematical Society, 1999), 57-72.

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  2. Kensaku Sakamoto, Daisuke Kiga, Ken Komiya, Hidetaka Gouzu, Shigeyuki Yokoyama, Shuji Ikeda, Hiroshi Sugiyama, and Masami Hagiya. State Transitions by Molecules. BioSystems, Vol.52, No.1-3, 1999, pp.81–91.

    Article  Google Scholar 

  3. K. Komiya, K. Sakamoto, H. Gouzu, S. Yokoyama, M. Arita, A. Nishikawa, and M. Hagiya, “Succesive State Transitions with I/O Interface by Molecules”, in (A. Condon and G. Rozenberg, Eds.) DNA Computing, Springer-Verlag LNCS, Vol.2054, (Springer, Berlin, 2001), 17–26.

    Google Scholar 

  4. David Harlan Wood, Hong Bi, Steven O. Kimbrough, Dongjun Wu, and Jumghuei Chen. DNA Starts to Lean Poker. DNA7, 7th International Meeting on DNA Based Computers, Preliminary Proceedings, 2001,pp.23–32.

    Google Scholar 

  5. Masayuki YAMAMURA, Yusuke HIROTO, and Taku MATOBA. Another Realization of Aqueous Computing with Peptide Nucleic Acid. DNA7, 7th International Meeting on DNA Based Computers, Preliminary Proceedings, 2001,pp.251–259.

    Google Scholar 

  6. J.A. Rose, R.J. Deaton, M. Hagiya, A. Suyama: An Equilibrium Analysis of the Efficiency of an Autonomous Molecular Computer, Physical Review E, Vol.65, No.2–1, 2002, 021910, pp.1–13.

    Article  Google Scholar 

  7. Richard D. Morgan, Celine Calvet, Matthew Demeter, Refael Agra Huimin Kong.Characterization of the Specific DNA Nicking Activity of Restriction Endonuclease N.BstNBT. Biol. Chem. Vol. 381, 1123–1125 (2000).

    Google Scholar 

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© 2003 Springer-Verlag Berlin Heidelberg

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Matsuda, D., Yamamura, M. (2003). Cascading Whiplash PCR with a Nicking Enzyme. In: Hagiya, M., Ohuchi, A. (eds) DNA Computing. DNA 2002. Lecture Notes in Computer Science, vol 2568. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36440-4_4

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  • DOI: https://doi.org/10.1007/3-540-36440-4_4

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-00531-5

  • Online ISBN: 978-3-540-36440-5

  • eBook Packages: Springer Book Archive

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