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Design of a Functional Nanomaterial with Recognition Ability for Constructing Light-Driven Nanodevices

  • Xingguo Liang
  • Toshio Mochizuki
  • Taiga Fujii
  • Hiromu Kashida
  • Hiroyuki Asanuma
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6518)

Abstract

An artificial macromolecule (foldamer) was designed as a novel nanomaterial with the backbone of phosphodiester and the side chain of functional molecules and nucleobases. The functional molecules tethered on D-threoninol and the nucleosides on D-ribose can be lined up with any sequence and ratio by using standard phosphoramidite chemistry. The nucleobases that form Watson-Crick base pairs provide the sequence recognition which is required for constructing complicate nanostructures. The multiple functional molecules give applicable and advanced functions such as photoresponsiveness when azobenzenes were used. Unexpectedly, a stable double helix was formed even in the case that the ratio of azobenzene molecules and base pairs was as high as 2:1. More interestingly, this artificial duplex showed high sequence specificity: the stability decreased greatly when a mismatched base pair was present. Furthermore, the formation and dissociation of the constructed artificial duplex were reversibly and completely modulated with light irradiation. By using this new nanomaterial, a variety of functional nanostructures and nanodevices are promising to be designed.

Keywords

nanodevice nucleobase photoregulation hybridization 

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References

  1. 1.
    Seeman, N.C., Lukeman, P.S.: Nucleic Acid Nanostructures: Bottom-Up Control of Geometry on the Nanoscale. Rep. Prog. Phys. 68, 237–270 (2005)CrossRefGoogle Scholar
  2. 2.
    Fujita, M., Tominaga, M., Hori, A., Therrien, B.: Coordination Assemblies from a Pd(II)-Cornered Square Complex. Acc. Chem. Res. 38, 369–378 (2005)CrossRefGoogle Scholar
  3. 3.
    Zheng, J.P., Birktoft, J.J., Chen, Y., Wang, T., Sha, R.J., Constantinou, P.E., Ginell, S.L., Mao, C.D., Seeman, N.C.: From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal. Nature 461, 74–77 (2001)CrossRefGoogle Scholar
  4. 4.
    Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and Autonomous Computing Machine Made of Biomolecules. Nature 414, 430–434 (2001)CrossRefGoogle Scholar
  5. 5.
    Hecht, S., Huc, I.: Foldamers: Structure, Properties, and Applications. Wiley-VCH Verlag GmBH & Co. KGaA, Weinheim (2007)CrossRefGoogle Scholar
  6. 6.
    Kay, E.R., Leigh, D.A., Zerbetto, F.: Synthetic Molecular Motors and Mechanical Machines. Angew. Chem., Int. Ed. 46, 72–191 (2007)CrossRefGoogle Scholar
  7. 7.
    Hamdi, M., Ferreira, A.: DNA nanorobotics. Microelectronics J. 39, 1051–1059 (2008)CrossRefGoogle Scholar
  8. 8.
    Shih, W.M., Quispe, J.D., Joyce, G.F.: A 1.7-Kilobase Single-Stranded DNA that Folds into a Nanoscale Octahedron. Nature 427, 618–621 (2004)CrossRefGoogle Scholar
  9. 9.
    Mirkin, C.A., Letsinger, R.L., Mucic, R.C., Storhoff, J.J.: A DNA-Based Method for Rationally Assembling Nanoparticles into Macroscopic Materials. Nature 382, 607–609 (1996)CrossRefGoogle Scholar
  10. 10.
    Sharma, J., Chhabra, R., Cheng, A., Brownell, J., Liu, Y., Yan, H.: Control of Self-Assembly of DNA Tubules Through Integration of Gold Nanoparticles. Science 323, 112–116 (2009)CrossRefGoogle Scholar
  11. 11.
    He, Y., Ye, T., Su, M., Zhang, C., Ribbe, A.E., Jiang, W., Mao, C.D.: Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198–201 (2008)CrossRefGoogle Scholar
  12. 12.
    Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M.M., Sander, B., Stark, H., Oliveira, C.L.P., Pedersen, J.S., Birkedal, V., Besenbacher, F., Gothelf, K.V., Kjems, J.: Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73–77 (2009)CrossRefGoogle Scholar
  13. 13.
    Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C., Neumann, J.L.: A DNA-Fuelled Molecular Machine Made of DNA. Nature 406, 605–608 (2000)CrossRefGoogle Scholar
  14. 14.
    Shin, J.S., Pierce, N.A.: A Synthetic DNA Walker for Molecular Transport. J. Am. Chem. Soc. 126, 10834–10835 (2004)CrossRefGoogle Scholar
  15. 15.
    Seeman, N.C.: From Genes to Machines: DNA Nanomechanical Devices. Trends. Biochem. Sci. 30, 119–125 (2005)CrossRefGoogle Scholar
  16. 16.
    Beissenhirtz, M.K., Willner, I.: DNA-Based Machines. Org. Biomol. Chem. 4, 3392–3401 (2006)CrossRefGoogle Scholar
  17. 17.
    Beyer, S., Simmel, F.C.: A Modular DNA Signal Translator for the Controlled Release of a Protein by an Aptamer. Nucleic Acid Res. 34, 1581–1587 (2006)CrossRefGoogle Scholar
  18. 18.
    Kutyavin, I.V., Afonina, I.A., Mills, A., Gorn, V.V., Lukhtanov, E.A., Belousov, E.S., Singer, M.J., Walburger, D.K., Lokhov, S.G., Gall, A.A., Dempcy, R., Reed, M.W., Meyer, R.B., Hedgpeth, J.: 3’-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res. 28, 655–661 (2000)CrossRefGoogle Scholar
  19. 19.
    Wang, K., Tang, Z., Yang, C.J., Kim, Y., Fang, X., Li, W., Wu, Y., Medley, C.D., Cao, Z., Li, J., Colon, P., Lin, H., Tan, W.: Molecular engineering of DNA: molecular beacons. Angew. Chem. Int. Ed. 47, 2–17 (2008)CrossRefGoogle Scholar
  20. 20.
    Kelley, S.O., Boon, E.M., Barton, J.K., Jackson, N.M., Hill, M.G.: Single-base mismatch detection based on charge transduction through DNA. Nucleic Acids Res. 27, 4830–4837 (2000)CrossRefGoogle Scholar
  21. 21.
    Mayer, G., Heckel, A.: Biologically active molecules with a “light switch”. Angew. Chem. Int. Ed. Eng. 45, 4900–4921 (2006)CrossRefGoogle Scholar
  22. 22.
    Asanuma, H., Liang, X.G., Nishioka, H., Matsunaga, D., Liu, M.Z., Komiyama, M.: Synthesis of Azobenzene-Tethered DNA for Reversible Photo-Regulation of DNA Functions: Hybridization and Transcription. Nat. Protocols 2, 203–212 (2007)CrossRefGoogle Scholar
  23. 23.
    Liang, X.G., Nishioka, H., Takenaka, N., Asanuma, H.: A DNA Nanomachine Powered by Light Irradiation. ChemBioChem. 9, 702–705 (2008)CrossRefGoogle Scholar
  24. 24.
    Liang, X.G., Nishioka, H., Takenaka, N., Asanuma, H.: Construction of Photon-Fueled DNA Nanomachines by Tethering Azobenzenes as Engines. In: Goel, A., Simmel, F.C., Sosík, P. (eds.) DNA 14. LNCS, vol. 5347, pp. 21–32. Springer, Heidelberg (2009)CrossRefGoogle Scholar
  25. 25.
    Zhou, M.G., Liang, X.G., Mochizuki, T., Asanuma, H.: A light-driven DNA nanomachine for efficiently photoswitching RNA digestion. Angew. Chem. Int. Ed. 49, 2167–2170 (2010)CrossRefGoogle Scholar
  26. 26.
    Asanuma, H., Shirasuka, K., Takarada, T., Kashida, H., Komiyama, M.: DNA-Dye Conjugates for Controllable H* Aggregation. J. Am. Chem. Soc. 125, 2217–2223 (2003)CrossRefGoogle Scholar
  27. 27.
    Kashida, H., Fujii, T., Asanuma, H.: Threoninol as a Scaffold of Dyes (Threoninol-nucleotide) and Their Stable Interstrand Clustering in Duplexes. Org. Biomol. Chem. 6, 2892–2899 (2008)CrossRefGoogle Scholar
  28. 28.
    Fujii, T., Kashida, H., Asanuma, H.: Analysis of Coherent Heteroclustering of Different Dyes by Use of Threoninol-Nucleotides for Comparison with the Molecular Exciton Theory. Chem. Eur. J. 15, 10092–10102 (2009)CrossRefGoogle Scholar
  29. 29.
    Liang, X.G., Mochizuki, T., Asanuma, H.: A Supra-Photoswitch Involving Sandwiched DNA Base Pairs and Azobenzenes for Light-Driven Nanostructures and Nanodevices. Small 5, 1761–1768 (2009)CrossRefGoogle Scholar
  30. 30.
    Liang, X.G., Nishioka, H., Mochizuki, T., Asanuma, H.: An interstrand-wedged duplex composed of alternating DNA base pairs and covalently attached intercalators. J. Mater. Chem. 20, 575–581 (2010)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Xingguo Liang
    • 1
  • Toshio Mochizuki
    • 1
  • Taiga Fujii
    • 1
  • Hiromu Kashida
    • 1
  • Hiroyuki Asanuma
    • 1
    • 2
  1. 1.Department of Molecular Design and Engineering, Graduate School of EngineeringNagoya UniversityChikusaJapan
  2. 2.Core Research for Evolution Science and Technology (CREST)Japan Science and, Technology Agency (JST)KawaguchiJapan

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