Skip to main content

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

Natural Computing volume 4, pages 103–126 (2005)Cite this article

Abstract

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.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

References

  • Yurke. Bernard et al. (2000) ArticleTitleA DNA-fuelled molecular machine made of DNA Nature 406 605–608 Occurrence Handle10.1038/35020524 Occurrence Handle10949296

    Article  PubMed  Google Scholar 

  • Mao. Chengde et al. (1999) ArticleTitleA nanomechanical device based on the B-Z transition of DNA Nature 397 144–146 Occurrence Handle10.1038/16437 Occurrence Handle9923675

    Article  PubMed  Google Scholar 

  • Flamm. Christoph et al. (2000) ArticleTitleRNA folding at elementary step resolution RNA 6 325–338 Occurrence Handle10.1017/S1355838200992161 Occurrence Handle10744018

    Article  PubMed  Google Scholar 

  • EB. Baum (1995) ArticleTitleBuilding an associative memory vastly larger than the brain Science 268 583–585 Occurrence Handle7725109

    PubMed  Google Scholar 

  • Simmel. Friedrich C. et al. (2001) ArticleTitleUsing DNA to construct and power a nanoactuator Physical Review E 63 041913 Occurrence Handle10.1103/PhysRevE.63.041913

    Article  Google Scholar 

  • Simmel. Friedrich C. et al. (2002) ArticleTitleA DNA-based molecular device switchable between three distinct mechanical states Applied Physics Letters 80 883–885 Occurrence Handle10.1063/1.1447008

    Article  Google Scholar 

  • Yan. Hao et al. (2002) ArticleTitleA robust DNA mechanical device controlled by hybridization topology Nature 145 62–65

    Google Scholar 

  • Allawi. Hatim T. et al. (1997) ArticleTitleThermodynamics and NMR of internal G· T mismatches in DNA Biochemistry 36 10581–10594 Occurrence Handle10.1021/bi962590c Occurrence Handle9265640

    Article  PubMed  Google Scholar 

  • Allawi. Hatim T. et al. (1998) ArticleTitleNearest neighbor thermodynamic parameters for internal G· A mismatches in DNA Biochemistry 37 2170–2179 Occurrence Handle10.1021/bi9724873 Occurrence Handle9485363

    Article  PubMed  Google Scholar 

  • Allawi. Hatim T. et al. (1998) ArticleTitleThermodynamics of internal C· T mismatches in DNA Nucleic Acids Research 26 2694–2701 Occurrence Handle10.1093/nar/26.11.2694 Occurrence Handle9592156

    Article  PubMed  Google Scholar 

  • Allawi. Hatim T. et al. (1998) ArticleTitleNearest-neighbor thermodynamics of internal A· C mismatches in DNA: Sequence dependence and pH effects Biochemistry 37 9435–9444 Occurrence Handle10.1021/bi9803729 Occurrence Handle9649326

    Article  PubMed  Google Scholar 

  • 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 92–96

  • Hofacker. Ivo L. et al. (1994) ArticleTitleFast folding and comparison of RNA secondary structures Monatshefte für Chemie (Chemical Monthly). 125 167–188

    Google Scholar 

  • JS. McCaskill (1990) ArticleTitleThe equilibrium partition function and base pair binding probabilities for RNA secondary structure Biopolymers 29 1105–1119 Occurrence Handle10.1002/bip.360290621 Occurrence Handle1695107

    Article  PubMed  Google Scholar 

  • SantaLucia John SuffixJr. (1998) ArticleTitleA unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proceeding of National Academy of Sciences USA 95 1460–1465 Occurrence Handle10.1073/pnas.95.4.1460

    Article  Google Scholar 

  • M. Zuker et al. (1981) ArticleTitleOptimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Research 9 133–148 Occurrence Handle6163133

    PubMed  Google Scholar 

  • Peyret. Nicolas et al. (1999) ArticleTitleNearest neighbor thermodynamics of DNA with A· A, C· C, G· G and T· T mismatches Biochemistry 38 3468–3477 Occurrence Handle10.1021/bi9825091 Occurrence Handle10090733

    Article  PubMed  Google Scholar 

  • Bommarito. Salvatore et al. (2000) ArticleTitleThermodynamic parameters for DNA sequences with dangling ends Nucleic Acids Research 28 1929–1934 Occurrence Handle10.1093/nar/28.9.1929 Occurrence Handle10756193

    Article  PubMed  Google Scholar 

  • Satoshi Kashiwamura. et al. (2002). Hierarchical DNA Memory Based on Nested PCR. Preliminary Proceedings of the Eighth International Meeting on DNA Based Computers 231–240

  • Wuchty. Stefan et al. (1999) ArticleTitleComplete suboptimal folding of RNA and the stability of secondary structures Biopolymers 49 145–165 Occurrence Handle10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G Occurrence Handle10070264

    Article  PubMed  Google Scholar 

  • Morgan. Steve R. et al. (1998) ArticleTitleBarrier heights between ground states in a model of RNA secondary structure J Phys A: Math Gen 31 3153–3170 Occurrence Handle10.1088/0305-4470/31/14/005

    Article  Google Scholar 

  • AJ. Turberfield et al. (2003) ArticleTitleDNA fuel for free-running nanomachines Physical Review Letters 90 11 Occurrence Handle10.1103/PhysRevLett.90.118102

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Japan Science and Technology Corporation (JST-CREST), Kawaguchi Center Building, 4-1-8 Honcho, Kawaguchi City, Saitama, 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. JAPAN PATENT OFFICE, 3-4-3 Kasumigaseki, Chiyoda-ku, Tokyo, 100-8915, Japan

    Hiroki Uejima

  4. JST-CREST and Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, Japan

    Masami Hagiya

  5. 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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masahito Yamamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hiroki Uejima
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Masami Hagiya
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kensaku Sakamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Azuma Ohuchi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Atsushi Kameda.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kameda, A., Yamamoto, M., Uejima, H. et al. Hairpin-based state machine and conformational addressing: Design and experiment. Nat Comput 4, 103–126 (2005). https://doi.org/10.1007/s11047-004-4007-y

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11047-004-4007-y

Keywords

  • DNA computing
  • molecular computing
  • molecluar machine
  • molecular memory