Photonic DNA Nano-Processor: A Photonics-Based Approach to Molecular Processing Mediated by DNA

  • Yusuke OguraEmail author
  • Takahiro Nishimura
  • Hirotsugu Yamamoto
  • Kenji Yamada
  • Jun Tanida
Part of the Nano-Optics and Nanophotonics book series (NON)


This chapter describes a photonic deoxyribonucleic acid (DNA) nano-processor, which is capable of dealing with molecules as real objects and with their associated information simultaneously in a bio-molecular environment. We present a light-activatable DNA nano-processor and DNA scaffold logic as implementation methods, and reveal their fundamental properties through experimental and analytical results.


Fluorescence Resonance Energy Transfer Visible Light Irradiation Photonic Signal Fluorescence Resonance Energy Transfer Signaling Fluorescence Resonance Energy Transfer Pair 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was supported by Grants-in-Aid for Scientific Research (B) (No. 22300103) and for Scientific Research on Innovative Areas “Nanomedicine Molecular Science” (No. 2306) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.


  1. 1.
    J.K. Willmann, N. Bruggen, L.M. Dinkelborg, S.S. Gambhir, Nat. Rev. Drug Discov. 7, 591 (2008)CrossRefGoogle Scholar
  2. 2.
    B. Huang, H. Babcock, X. Zhuang, Cell 143, 1047 (2010)CrossRefGoogle Scholar
  3. 3.
    N.C. Seeman, Annu. Rev. Biochem. 79, 65 (2010)CrossRefGoogle Scholar
  4. 4.
    E. Winfree, F. Liu, L.A. Wenzler, N.C. Seeman, Nature 394, 539 (1998)ADSCrossRefGoogle Scholar
  5. 5.
    P.W.K. Rothemund, Nature 440, 297 (2006)ADSCrossRefGoogle Scholar
  6. 6.
    E.S. Andersen, M. Dong, M.M. Nielsen, K. Jahn, R. Subramani, W. Mamdouh, M.M. Golas, B. Sander, H. Stark, C.L.P. Oliveira, J.S. Pedersen, V. Birkedal, F. Besenbacher, K.V. Gothelf, J Kjems. Nature 459, 73 (2009)ADSCrossRefGoogle Scholar
  7. 7.
    S.H. Park, P. Yin, Y. Liu, J.H. Reif, T.H. LaBean, H. Yan, Nano Lett. 5, 729 (2005)ADSCrossRefGoogle Scholar
  8. 8.
    W. Chongchitmate, C. Dwyer, A.R. Lebeck, IEEE Micro 30, 110 (2010)Google Scholar
  9. 9.
    B. Yurke, A.J. Turberfield, A.P. Mills Jr, F.C. Simmel, J.L. Neumann, Nature 406, 605 (2000)ADSCrossRefGoogle Scholar
  10. 10.
    W.B. Sherman, N.C. Seeman, Nano Lett. 4, 1203 (2004)ADSCrossRefGoogle Scholar
  11. 11.
    J. Bath, A.J. Turberfield, Nature Nanotechnol. 2, 275 (2007)ADSCrossRefGoogle Scholar
  12. 12.
    L.M. Adleman, Science 266, 1021 (1994)ADSCrossRefGoogle Scholar
  13. 13.
    Y. Benenson, B. Gil, U. Ben-Dor, R. Adar, E. Shapiro, Nature 429, 423 (2004)ADSCrossRefGoogle Scholar
  14. 14.
    M.N. Stojanovic, D. Stefanovic, Nat. Biotechnol. 21, 1069 (2003)CrossRefGoogle Scholar
  15. 15.
    G. Seelig, D. Soloveichik, D.Y. Zhang, E. Winfree, Science 314, 1585 (2006)ADSCrossRefGoogle Scholar
  16. 16.
    L. Qian, E. Winfree, J. Bruck, Nature 475, 368 (2011)CrossRefGoogle Scholar
  17. 17.
    P.W.K. Rothemund, N. Papadakis, E. Winfree, PLoS Biol. 2, 2041 (2004)Google Scholar
  18. 18.
    J. Elbaz, O. Lioubashevski, F. Wang, F. Remacle, R.D. Levine, I. Willner, Nature Nanotech. 5, 417 (2010)ADSCrossRefGoogle Scholar
  19. 19.
    P. Cheben (ed.), Proceedings of 2011 ICO International Conference on Information Photonics (on CD-ROM), Ottawa, 2011.Google Scholar
  20. 20.
    T. Nishimura, Y. Ogura, K. Yamada, H. Yamamoto, J. Tanida, Proc. SPIE 8102, 810207 (2011)CrossRefGoogle Scholar
  21. 21.
    T. Nishimura, Y. Ogura, K. Yamda, H. Yamamoto, J. Tanida, in Abstracts for 8th Annual Conference on Foundations of Nanoscience (Snowbird Cliff Lodge, Snowbird, Utah, April, 2011), pp. 181–182Google Scholar
  22. 22.
    H. Asanuma, X. Liang, H. Nishioka, D. Matsunaga, M. Liu, M. Komiyama, Nat. Protocols 2, 203 (2007)CrossRefGoogle Scholar
  23. 23.
    X. Liang, H. Nishioka, N. Takenaka, H. Asanuma, ChemBioChem 9, 702 (2008)CrossRefGoogle Scholar
  24. 24.
    Y. Ogura, T. Nishimura, J. Tanida, Appl. Phys. Express 2, 025004 (2009)ADSCrossRefGoogle Scholar
  25. 25.
    C. Wang, Z. Zhu, Y. Song, H. Lin, C.J. Yang, W. Tan, Chem. Commun. 47, 5708 (2011)CrossRefGoogle Scholar
  26. 26.
    T. Nishimura, Y. Ogura, J. Tanida, Biomed. Opt. Express 3, 920 (2012)CrossRefGoogle Scholar
  27. 27.
    T. Nishimura, Y. Ogura, J. Tanida, Appl. Phys. Lett. 101, 233703 (2012)ADSCrossRefGoogle Scholar
  28. 28.
    W. H. Press, B. P. Flannery, S. A. Teukolsky, W. T. Vetterling, Numerical Recipes in FORTRAN: The Art of Scientific Computing, 2nd ed. (Cambridge, England: Cambridge University Press, 1992), pp. 704–708.Google Scholar
  29. 29.
    T. Nishimura, Y. Ogura, J. Tanida, Appl. Phys. Express 6, 015201 (2013)ADSCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Yusuke Ogura
    • 1
    Email author
  • Takahiro Nishimura
    • 1
  • Hirotsugu Yamamoto
    • 2
  • Kenji Yamada
    • 3
  • Jun Tanida
    • 1
  1. 1.Graduate School of Information Science and TechnologyOsaka UniversitySuitaJapan
  2. 2.Department of Optical Science and TechnologyThe University of TokushimaTokushimaJapan
  3. 3.Graduate School of MedicineOsaka UniversitySuitaJapan

Personalised recommendations