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Unravel four hairpins!

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Abstract

DNA machines consisting of consecutive hairpins, which we have previously described, have various potential applications in DNA computation. In the present study, a 288-base DNA machine containing four consecutive hairpins was successfully constructed by ligation and PCR. PAGE and fluorescence spectroscopy experiments verified that all four hairpins were successfully opened by four opener oligomers, and that hairpin opening was dependent on the proper openers added in the correct order. Quantitative analysis of the final results by fluorescence spectroscopy indicated that all four hairpins were open in about 1/4 to 1/3 of the DNA machines.

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Acknowledgement

The work presented in this paper was partially supported by Grand-in-Aid for Scientific Research on Priority Area No. 14085202, Ministry of Education, Culture, Sports, Science and Technology, Japan.

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Authors and Affiliations

  1. Japan Science and Technology Corporation, Kawaguchi Center Building, 4-1-8 Honcho, Kawaguchi City, Saitama, 332-0012, Japan

    Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Satsuki Yaegashi & Masami Hagiya

  2. Graduate School of Information Science and Technology, 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

    Masami Hagiya

Authors
  1. Atsushi Kameda
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  2. Masahito Yamamoto
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  3. Azuma Ohuchi
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  4. Satsuki Yaegashi
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  5. Masami Hagiya
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Corresponding author

Correspondence to Masami Hagiya.

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Kameda, A., Yamamoto, M., Ohuchi, A. et al. Unravel four hairpins!. Nat Comput 7, 287–298 (2008). https://doi.org/10.1007/s11047-007-9035-y

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  • DOI: https://doi.org/10.1007/s11047-007-9035-y

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