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Programmable self-assembly of metal ions inside artificial DNA duplexes

Nature Nanotechnology volume 1, pages 190–194 (2006)Cite this article

An Erratum to this article was published on 05 December 2006

Abstract

The ultimate bottom-up approach for the construction of functional nanosystems requires the precise arrangement of atoms and molecules in three dimensions. DNA is currently one of the most prominent molecules able to self-assemble into complex networks1,2 and is therefore regarded as the ‘silicon of the nano-world’3. Metals and metal ions, in contrast, are the atomic building-blocks needed in such materials to establish functions such as electrical conductivity or magnetism. Here we report a new concept, which efficiently combines metal ions and DNA. The DNA structure is used as a matrix to program robustly the complexation of different metal ions under precise control with regard to element, number and composition.

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Figure 1
Figure 2: Assembly of Cu2+ and Hg2+ ions through duplex formation of d(5′-GHPHC-3′).
Figure 3: Schematic representation of the use of a combination of salicylic aldehyde-salicylic aldehyde (S–S) and thymine-thymine (T–T) mismatches for the assembly of a heterogeneous metal stack consisting of S–Cu2+(en)–S and T–Hg2+–T base pairs.
Figure 4: Assembly of Cu2+ and Hg2+ ions into duplex d(5′-CGGCCTSSSSTTTTSCGCGC-3′)·d(3′-GCCGGTSSSSTTTTSGCGCG-5′).

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References

  1. Gothelf, K. V. & LaBean, T. H. DNA-programmed assembly of nanostructures. Org. Biomol. Chem. 3, 4023–4037 (2005).

    Article  CAS  Google Scholar 

  2. Tanaka, K. & Shionoya, M. Bio-inspired programmable self-assembly on DNA templates. Chem. Lett. 35, 694–699 (2006).

    Article  CAS  Google Scholar 

  3. Luo, D & Li Y. Nucleic acid engineered nanomaterials and their applications. Handbook of Nanostructured Biomaterials and their Applications in Nanobiotechnology 2, 223–345 (American Scientific Publishers, Stevenson Ranch, 2005).

    Google Scholar 

  4. Marquis, A. et al. Messages in molecules: ligand/cation coding and self-recognition in a constitutionally dynamic system of heterometallic double helicates. Chem. Eur. J. 12, 5632–5641 (2006).

    Article  CAS  Google Scholar 

  5. Gait, K. J. (ed.) Oligonucleotide Synthesis: A Practical Approach (IRL Press, New York, 1990).

    Google Scholar 

  6. Tanaka, K. et al. A discrete self-assembled metal array in artificial DNA. Science 299, 1212–1213 (2003).

    Article  CAS  Google Scholar 

  7. Tanaka, K. & Shionoya, M. Synthesis of a novel nucleoside for alternative DNA base pairing through metal complexation. J. Org. Chem. 64, 5002–5003 (1999).

    Article  CAS  Google Scholar 

  8. Tanaka, K. et al. Efficient incorporation of a copper hydroxypyridone base pair in DNA. J. Am. Chem. Soc. 124, 12494–12498 (2002).

    Article  CAS  Google Scholar 

  9. Tanaka, K., Yamada, Y. & Shionoya, M. Formation of silver(I)-mediated DNA duplex and triplex through an alternative base pair of pyridine nucleobases. J. Am. Chem. Soc. 124, 8802–8803 (2002).

    Article  CAS  Google Scholar 

  10. Clever, G. H., Polborn, K. & Carell, T. A highly DNA-duplex-stabilizing metal–salen base pair. Angew. Chem., Int. Ed. 44, 7204–7208 (2005).

    Article  CAS  Google Scholar 

  11. Clever, G. H. et al. Metal salen-base-pair complexes inside DNA: complexation overrides sequence information. Chem. Eur. J. DOI: 12, 8708–8718 (2006).

    Article  CAS  Google Scholar 

  12. Meggers, E. et al. A novel copper-mediated DNA base pair. J. Am. Chem. Soc. 122, 10714–10715 (2000).

    Article  CAS  Google Scholar 

  13. Zimmermann, N., Meggers, E. & Schultz, P. G. A novel silver(I)-mediated DNA base pair. J. Am. Chem. Soc. 124, 13684–13685 (2002).

    Article  CAS  Google Scholar 

  14. Weizman, H. & Tor, Y. 2,2′-Bipyridine ligandoside: a novel building block for modifying DNA with intra-duplex metal complexes. J. Am. Chem. Soc. 123, 3375–3376 (2001).

    Article  CAS  Google Scholar 

  15. Switzer, C., Sinha, S., Kim, P. H. & Heuberger, B. D. A purine-like nickel(II) base pair for DNA. Angew. Chem., Int. Ed. 44, 1529–1532 (2005).

    Article  CAS  Google Scholar 

  16. Kuklenyik, Z. & Marzilli, L. G. Mercury(II) site-selective binding to a DNA hairpin. Relationship of sequence-dependent intra- and interstrand cross-linking to the hairpin-duplex conformational transition. Inorg. Chem. 35, 5654–5662 (1996).

    Article  CAS  Google Scholar 

  17. Miyake, Y. et al. MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes. J. Am. Chem. Soc. 128, 2172–2173 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was partially supported by Grant-in-Aids for Young Scientists (A) to K.T., Priority Area to K.T. and M.S., Scientific Research (S) to M.S., and the 21st Century COE Program for Frontiers in Fundamental Chemistry to M.S. from the Ministry of Education, Culture, Sports, Science and Technology (Japan), The Toray Science Foundation to K.T. and the Deutsche Forschungsgemeinschaft (DFG) to T.C., as well as the Volkswagen Foundation. G.H.C. acknowledges the Funds of the German Chemical Industry for a pre-doctoral Fellowship.

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Author notes

  1. Kentaro Tanaka and Guido H. Clever: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Chemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

    Kentaro Tanaka, Yusuke Takezawa, Yasuyuki Yamada & Mitsuhiko Shionoya

  2. PRESTO, Japan Science and Technology Agency (JST), 4-1-8, Honcho, Kawaguchi-shi, 332-0012, Saitama, Japan

    Kentaro Tanaka

  3. Department of Chemistry and Biochemistry, Ludwig-Maximilians-University Munich, Butenandtstrasse 5–13, Haus F, München, 81377, Germany

    Guido H. Clever, Corinna Kaul & Thomas Carell

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  1. Kentaro Tanaka
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Contributions

K.T., G.H.C., M.S. and T.C. planned the project and analyzed the experimental data. K.T., Y.T., Y.Y. performed the experiments on the duplexes containing the hydroxypyridone ligands and G.H.C. and K.C. performed the experiments on the duplexes containing the salen ligand.

Corresponding authors

Correspondence to Mitsuhiko Shionoya or Thomas Carell.

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The authors declare no competing financial interests.

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Tanaka, K., Clever, G., Takezawa, Y. et al. Programmable self-assembly of metal ions inside artificial DNA duplexes. Nature Nanotech 1, 190–194 (2006). https://doi.org/10.1038/nnano.2006.141

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