Natural Computing

, Volume 7, Issue 2, pp 287–298 | Cite as

Unravel four hairpins!

  • Atsushi Kameda
  • Masahito Yamamoto
  • Azuma Ohuchi
  • Satsuki Yaegashi
  • Masami Hagiya
Article

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.

Keywords

DNA computing DNA nanotechnology Molecular computing Molecular memory Molecular machine 

References

  1. Dirks RM, Pierce NA (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci 101(43):15275–15278CrossRefGoogle Scholar
  2. Hagiya M, Yaegashi S, Takahashi K (2005) Computing with Hairpins and Secondary Structures of DNA. In: Nanotechnology: science and computation, Natural computing series. Springer, pp 293–308Google Scholar
  3. Kameda A, Yamamoto M, Uejima H, Hagiya M, Sakamoto K, Ohuchi A (2005) Hairpin-based state machine and conformational addressing: design and experiment. Nat Comput 4(2):103–126CrossRefMathSciNetGoogle Scholar
  4. Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302CrossRefGoogle Scholar
  5. Seelig G, Yurke B, Winfree E (2005) DNA Hybridization catalysts and catalyst circuits. In: DNA computing, 10th international workshop on DNA computing. Lecture Notes in Computer Science, vol 3384, pp 329–343Google Scholar
  6. Takahashi K, Yaegashi S, Kameda A, Hagiya M (2006) Chain reaction systems based on loop dissociation of DNA. In: DNA computing: 11th international workshop on DNA computing, DNA11. Lecture Notes in Computer Science, vol 3892, pp 347–358Google Scholar
  7. Takahashi N, Kameda A, Yamamoto M, Ohuchi A (2005) Aqueous computing with DNA hairpin-based RAM. In: DNA computing, 10th international workshop on DNA computing. Lecture Notes in Computer Science, vol 3384, pp 355–364Google Scholar
  8. Uejima H, Hagiya M (2004) Secondary structure design of multi-state DNA machines based on sequential structure transitions. In: DNA computing, 9th international workshop on DNA-based computers. Lecture Notes in Computer Science. Springer, vol 2943, pp 74–85Google Scholar
  9. Yan H (2005) An inexpensive LED-based fluorometer used to study a hairpin-based DNA nanomachine. In: DNA computing, 10th international workshop on DNA computing. Lecture Notes in Computer Science, vol 3384, pp 399–409Google Scholar
  10. Yurke B, Turberfield AJ, Mills Jr AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605–608CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Atsushi Kameda
    • 1
  • Masahito Yamamoto
    • 1
    • 2
  • Azuma Ohuchi
    • 1
    • 2
  • Satsuki Yaegashi
    • 1
  • Masami Hagiya
    • 1
    • 3
  1. 1.Japan Science and Technology CorporationKawaguchi City, SaitamaJapan
  2. 2.Graduate School of Information Science and TechnologyHokkaido UniversityKita-ku, SapporoJapan
  3. 3.Department of Computer Science, Graduate School of Information Science and TechnologyUniversity of TokyoTokyoJapan

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