Natural Computing

, Volume 4, Issue 2, pp 103–126 | Cite as

Hairpin-based state machine and conformational addressing: Design and experiment

  • Atsushi Kameda
  • Masahito Yamamoto
  • Hiroki Uejima
  • Masami Hagiya
  • Kensaku Sakamoto
  • Azuma Ohuchi


In this paper, we propose a new architecture for a multi-state DNA machine whose conformation of repeated hairpin structures changes sequentially in response to input oligomers. As an application of the machine, we also propose molecular memory in which the machine is used as a memory unit. Addressing in the memory is realized through state transitions of the machine. We then describe a method for designing DNA sequences of the machine, which exhaustively checks conformational changes of the machine by dividing its secondary structure into hairpin units. The method is based on the minimum free energy of the structure, the structure transition paths, and the total frequency of optimal and suboptimal structures. DNA sequences designed by the method were tested in a chemical experiment in which a machine consisting of two hairpins was actually constructed. As a result, we verified that the multi-state DNA machine realized the expected changes in its secondary structure.


DNA computing molecular computing molecluar machine molecular memory 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bernard, Yurke.,  et al. 2000A DNA-fuelled molecular machine made of DNANature406605608CrossRefPubMedGoogle Scholar
  2. Chengde, Mao.,  et al. 1999A nanomechanical device based on the B-Z transition of DNANature397144146CrossRefPubMedGoogle Scholar
  3. Christoph, Flamm.,  et al. 2000RNA folding at elementary step resolutionRNA6325338CrossRefPubMedGoogle Scholar
  4. Baum, EB. 1995Building an associative memory vastly larger than the brainScience268583585PubMedGoogle Scholar
  5. Friedrich C., Simmel.,  et al. 2001Using DNA to construct and power a nanoactuatorPhysical Review E63041913CrossRefGoogle Scholar
  6. Friedrich C., Simmel.,  et al. 2002A DNA-based molecular device switchable between three distinct mechanical statesApplied Physics Letters80883885CrossRefGoogle Scholar
  7. Hao, Yan.,  et al. 2002A robust DNA mechanical device controlled by hybridization topologyNature1456265Google Scholar
  8. Hatim T., Allawi.,  et al. 1997Thermodynamics and NMR of internal G· T mismatches in DNABiochemistry361058110594CrossRefPubMedGoogle Scholar
  9. Hatim T., Allawi.,  et al. 1998Nearest neighbor thermodynamic parameters for internal G· A mismatches in DNABiochemistry3721702179CrossRefPubMedGoogle Scholar
  10. Hatim T., Allawi.,  et al. 1998Thermodynamics of internal C· T mismatches in DNANucleic Acids Research2626942701CrossRefPubMedGoogle Scholar
  11. Hatim T., Allawi.,  et al. 1998Nearest-neighbor thermodynamics of internal A· C mismatches in DNA: Sequence dependence and pH effectsBiochemistry3794359444CrossRefPubMedGoogle Scholar
  12. Hiroki Uejima. et al. (2003). Analyzing the secondary structure transition paths of DNA/RNA molecules. Proceedings of Ninth Annual International Meeting on DNA Based Computers 92–96Google Scholar
  13. Ivo L., Hofacker.,  et al. 1994Fast folding and comparison of RNA secondary structuresMonatshefte für Chemie (Chemical Monthly).125167188Google Scholar
  14. McCaskill, JS. 1990The equilibrium partition function and base pair binding probabilities for RNA secondary structureBiopolymers2911051119CrossRefPubMedGoogle Scholar
  15. John, SantaLucia,Jr. 1998A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamicsProceeding of National Academy of Sciences USA9514601465CrossRefGoogle Scholar
  16. Zuker, M.,  et al. 1981Optimal computer folding of large RNA sequences using thermodynamics and auxiliary informationNucleic Acids Research9133148PubMedGoogle Scholar
  17. Nicolas, Peyret.,  et al. 1999Nearest neighbor thermodynamics of DNA with A· A, C· C, G· G and T· T mismatchesBiochemistry3834683477CrossRefPubMedGoogle Scholar
  18. Salvatore, Bommarito.,  et al. 2000Thermodynamic parameters for DNA sequences with dangling endsNucleic Acids Research2819291934CrossRefPubMedGoogle Scholar
  19. Satoshi Kashiwamura. et al. (2002). Hierarchical DNA Memory Based on Nested PCR. Preliminary Proceedings of the Eighth International Meeting on DNA Based Computers 231–240Google Scholar
  20. Stefan, Wuchty.,  et al. 1999Complete suboptimal folding of RNA and the stability of secondary structuresBiopolymers49145165CrossRefPubMedGoogle Scholar
  21. Steve R., Morgan.,  et al. 1998Barrier heights between ground states in a model of RNA secondary structureJ Phys A: Math Gen3131533170CrossRefGoogle Scholar
  22. Turberfield, AJ.,  et al. 2003DNA fuel for free-running nanomachinesPhysical Review Letters9011118102CrossRefGoogle Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  • Atsushi Kameda
    • 1
  • Masahito Yamamoto
    • 2
  • Hiroki Uejima
    • 3
  • Masami Hagiya
    • 4
  • Kensaku Sakamoto
    • 5
  • Azuma Ohuchi
    • 2
  1. 1.Japan Science and Technology Corporation (JST-CREST)Kawaguchi CityJapan
  2. 2.Division of Systems and Information EngineeringGraduate School of Engineering Hokkaido UniversitySapporoJapan
  3. 3.JAPAN PATENT OFFICEChiyoda-kuJapan
  4. 4.JST-CREST and Department of Computer Science, Graduate School of Information Science and TechnologyUniversity of TokyoJapan
  5. 5.Department of Biophysics and Biochemistry, Graduate School of ScienceUniversity of TokyoBunkyo-kuJapan

Personalised recommendations