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International Workshop on DNA-Based Computers

DNA 2003: DNA Computing pp 219–224Cite as

Conformational Addressing Using the Hairpin Structure of Single-Strand DNA

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Part of the Lecture Notes in Computer Science book series (LNCS,volume 2943)

Abstract

In this paper, we demonstrate through a chemistry experiment that conformational addressing can be achieved using the hairpin structure of a DNA molecule. The hairpin structure made by single-strand DNA (ssDNA) self-hybridization is made into the address part of conformational addressing, and it is assumed that the memory is read by opening this hairpin. The hairpin is continuously arranged in order to divide the address by class. Reading a sub-address requires an appropriate input oligomer to be added, when the preceding hairpin has been opened. We investigated, through the chemistry experiment, whether it would be possible to open the hairpin by the addition of an input oligomer into a solution that contained a hairpin-formed ssDNA.

Keywords

  • Data Block
  • Hairpin Structure
  • Stem Portion
  • Address Block
  • ssDNA Molecule

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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  • DOI: 10.1007/978-3-540-24628-2_22
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References

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Author information

Authors and Affiliations

  1. Japan Science and Technology Cooperation (JST), Honmachi 4-1-8, Kawaguchi, 332-0012, Japan

    Atsushi Kameda

  2. Division of Systems and Information Engineering, Graduate School of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, 060-8628, Japan

    Masahito Yamamoto & Azuma Ohuchi

  3. Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan

    Hiroki Uejima & Masami Hagiya

  4. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan

    Kensaku Sakamoto

Authors
  1. Atsushi Kameda
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  2. Masahito Yamamoto
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  3. Hiroki Uejima
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  4. Masami Hagiya
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  5. Kensaku Sakamoto
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  6. Azuma Ohuchi
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Editor information

Editors and Affiliations

  1. Department of Chemistry, New York University, 10003, New York, NY, USA

    Junghuei Chen

  2. Department of Computer Science, Duke University, Durham, NC, USA

    John Reif

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© 2004 Springer-Verlag Berlin Heidelberg

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Cite this paper

Kameda, A., Yamamoto, M., Uejima, H., Hagiya, M., Sakamoto, K., Ohuchi, A. (2004). Conformational Addressing Using the Hairpin Structure of Single-Strand DNA. In: Chen, J., Reif, J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24628-2_22

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  • DOI: https://doi.org/10.1007/978-3-540-24628-2_22

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-20930-0

  • Online ISBN: 978-3-540-24628-2

  • eBook Packages: Springer Book Archive