Natural Computing

, Volume 7, Issue 3, pp 371–383 | Cite as

Multi-fueled approach to DNA nano-robotics

  • Akio Nishikawa
  • Satsuki Yaegashi
  • Fumiaki Tanaka
  • Kazumasa Ohtake
  • Masami Hagiya
Article

Abstract

An approach to multi-fueled DNA nano-robotics is described. We propose three types of driving force (i.e., fuel for DNA nano-robots): thermal fuel, pH fuel, and light fuel. The thermal fuel controls the hybridization of DNA molecules around the melting temperature. The pH fuel controls the hybridization of the so-called i-motif by changing the pH condition. The light fuel controls the hybridization of DNA oligomers that are intercalated with azobenzene by irradiation with UV or visible light. These three fuels are not mutually exclusive. However, experimental conditions for the fueling of DNA nano-robots show efficacy. Concrete ideas for using these three fuel types are proposed and discussed. In addition, the results of calibration experiments and preliminary results for refining pH fuel sequence are also shown.

Keywords

Azobenzene DNA Nano-robotics i-Motif Light fuel Multi-fueled approach pH Fuel Thermal fuel 

Abbreviations

BHQ2

Stands for Black Hole Quencher type2

RG

Stands for Rhodamine Green fluorescence group

References

  1. Alberti P, Mergny JL (2003) DNA duplex-quadruplex exchange as the basis for a nanomolecular machine. Proc Natl Acad Sci USA 100:1569–1573CrossRefGoogle Scholar
  2. Asanuma H et al (1999) Photoregulation of the formation and dissociation of a DNA duplex by using the cis-trans isomerization of azobenzene. Angew Chem 38:2293–2395Google Scholar
  3. Asanuma H et al (2003) Photo-regulation of DNA function by azobenzene-tethered oligonucleotides. Nucleic Acids Res 3(Suppl):117–118Google Scholar
  4. Chen Y, Mao C (2004) Putting a brake on an autonomous DNA nanomotor. J Am Chem Soc 126:8626–8627CrossRefGoogle Scholar
  5. Chen Y, Lee SH, Mao C (2004) A DNA nanomachine based on a duplex-triplex transition. Angew Chem Int Ed 43:5335–5338CrossRefGoogle Scholar
  6. Dittmer WU, Reuter A, Simmel FC (2004) A DNA-based machine that can cyclically bind and release thrombin. Angew Chem Int Ed 43:3550–3553CrossRefGoogle Scholar
  7. Li JJ, Tan W (2002) A single DNA molecule nanomotor. Nano Lett 2:315–318Google Scholar
  8. Liu D, Balasubramanian S (2003) A proton-fuelled DNA nanomachine. Angew Chem 115:5912–5914CrossRefGoogle Scholar
  9. Mao C, Sun W, Shen Z, Seeman NC (1999) A DNA nanomechanical device based on the B–Z transition. Nature 397:144–146CrossRefGoogle Scholar
  10. Nutiu R, Li Y (2005) A DNA-protein nanoengine for “on-demand” release and precise delivery of molecules. Angew Chem Int Ed 44:5464–5467CrossRefGoogle Scholar
  11. Peyret N, SantaLucia J Jr (1999) HYTHER Ver. 1.0 [computer program]. Wayne State University, Detroit, MIGoogle Scholar
  12. Peyret N, Seneviratne PA, Allawi HT, SantaLucia J Jr (1999) Nearestneighbor thermodynamics and NMR of DNA sequences withinternal A.A, C.C, G.G, and T.T mismatches. Biochemistry 38:3468–3477CrossRefGoogle Scholar
  13. SantaLucia J Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95:1460–1465CrossRefGoogle Scholar
  14. Shin J-S, Pierce NA (2004) A synthetic DNA walker for molecular transport. J Am Chem Soc 126:10834–10835CrossRefGoogle Scholar
  15. Takahashi K, Yaegashi S, Asanuma H, Hagiya M (2006) Photo- and thermoregulation of DNA nanomachines. Lect Notes Comput Sci 3892:336–346CrossRefGoogle Scholar
  16. Tian Y, He Y, Chen Y, Yin P, Mao C (2005) A DNAzyme that walks processively and autonomously along a one-dimensional track. Angew Chem Int Ed 44:4355–4358CrossRefGoogle Scholar
  17. Yurke B, Turberfield AJ, Mills AP Jr, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Akio Nishikawa
    • 1
  • Satsuki Yaegashi
    • 2
  • Fumiaki Tanaka
    • 3
    • 2
  • Kazumasa Ohtake
    • 4
    • 2
  • Masami Hagiya
    • 3
    • 2
  1. 1.Department of EconomicsFuji UniversityHanamakiJapan
  2. 2.Core Research for Evolution Science and Technology (CREST) Japan Science and Technology Agency (JST)KawaguchiJapan
  3. 3.Department of Computer ScienceUniversity of TokyoTokyoJapan
  4. 4.Department of BiochemistryUniversity of TokyoTokyoJapan

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