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Enzyme cascades activated on topologically programmed DNA scaffolds

Nature Nanotechnology volume 4, pages 249–254 (2009)Cite this article

Abstract

The ability of DNA to self-assemble into one-, two- and three-dimensional nanostructures1,2,3,4,5,6,7,8,9,10,11,12,13,14, combined with the precision that is now possible when positioning nanoparticles15,16,17,18,19 or proteins20,21,22,23,24 on DNA scaffolds, provide a promising approach for the self-organization of composite nanostructures25,26,27. Predicting and controlling the functions that emerge in self-organized biomolecular nanostructures is a major challenge in systems biology, and although a number of innovative examples have been reported28,29,30, the emergent properties of systems in which enzymes are coupled together have not been fully explored. Here, we report the self-assembly of a DNA scaffold made of DNA strips that include ‘hinges’ to which biomolecules can be tethered. We attach either two enzymes or a cofactor–enzyme pair to the scaffold, and show that enzyme cascades or cofactor-mediated biocatalysis can proceed effectively; similar processes are not observed in diffusion-controlled homogeneous mixtures of the same components. Furthermore, because the relative position of the two enzymes or the cofactor–enzyme pair is determined by the topology of the DNA scaffold, it is possible to control the reactivity of the system through the design of the individual DNA strips. This method could lead to the self-organization of complex multi-enzyme cascades.

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Figure 1: Assembly of hexagon-like DNA strips and their structural imaging.
Figure 2
Figure 3: Assembly of enzyme cascades or cofactor–enzyme cascades on hexagon-like DNA scaffolds, their imaging and their functional characterization.

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References

  1. Seeman, N. C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982).

    CAS  Google Scholar 

  2. Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829–831 (1983).

    Article  CAS  Google Scholar 

  3. Mao, C., Sun, W. & Seeman, N. C. Designed two-dimensional DNA Holliday junction arrays visualised by atomic force microscopy. J. Am. Chem. Soc. 121, 5437–5443 (1999).

    Article  CAS  Google Scholar 

  4. Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998).

    Article  CAS  Google Scholar 

  5. Yang, X., Wenzler, L. A., Qi, J., Li, X. & Seeman, N. C. Ligation of DNA triangles containing double crossover molecules. J. Am. Chem. Soc. 120, 9779–9786 (1998).

    Article  CAS  Google Scholar 

  6. Ding, B., Sha, R. & Seeman, N. C. Pseudohexagonal 2D crystals from double crossover cohesion. J. Am. Chem. Soc. 126, 10230–10231 (2004).

    Article  CAS  Google Scholar 

  7. Park, S. H., Finkelstein, G. & LaBean, T. H. Stepwise self-assembly of DNA tile lattices using dsDNA bridges. J. Am. Chem. Soc. 130, 40–41 (2008).

    Article  CAS  Google Scholar 

  8. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article  CAS  Google Scholar 

  9. Zhang, C., He, Y., Chen, Y., Ribbe, A. E. & Mao, C. Aligning one-dimensional DNA duplexes into two-dimensional crystals. J. Am. Chem. Soc. 129, 14134–14135 (2007).

    Article  CAS  Google Scholar 

  10. Chen, J. & Seeman, N. C. Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–633 (1991).

    Article  CAS  Google Scholar 

  11. Mao, C., Sun, W. & Seeman, N. C. Assembly of Borromean rings from DNA. Nature 386, 137–138 (1997).

    Article  CAS  Google Scholar 

  12. Kuzuya, A., Wang, R., Sha, R. & Seeman, N. C. Six-helix and eight-helix DNA nanotubes assembled from half-tubes. Nano Lett. 7, 1757–1763 (2007).

    Article  CAS  Google Scholar 

  13. Faisal, A. A. & Sleiman, H. F. Modular access to structurally switchable 3D discrete DNA assemblies. J. Am. Chem. Soc. 129, 13376–13377 (2007).

    Article  Google Scholar 

  14. Simmel, F. C. Three-dimensional nanoconstruction with DNA. Angew. Chem. Int. Ed. 47, 5884–5887 (2008).

    Article  CAS  Google Scholar 

  15. Le, J. D. et al. DNA-templated self-assembly of metallic nanocomponents arrays on a surface. Nano Lett. 4, 2343–2347 (2004).

    Article  CAS  Google Scholar 

  16. Nykypanchuk, D., Maye, M. M., van der Lelie, D. & Gang, O. DNA-guided crystallization of colloidal nanoparticles. Nature 451, 549–552 (2008).

    Article  CAS  Google Scholar 

  17. Park, S. Y. et al. DNA-programmable nanoparticle crystallization. Nature 451, 553–556 (2008).

    Article  CAS  Google Scholar 

  18. Sharma, J. et al. DNA-tile-directed self-assembly of quantum dots into two-dimensional nanopatterns. Angew. Chem. Int. Ed. 47, 5157–5159 (2008).

    Article  CAS  Google Scholar 

  19. Li, H., Park, S. H., Reif, J. H., LaBean, T. H. & Yan, H. DNA templated self-assembly of protein and nanoparticle linear arrays. J. Am. Chem. Soc. 126, 418–419 (2004).

    Article  CAS  Google Scholar 

  20. Yan, H., Park, S. H., Finkelstein, G., Reif, J. H. & LaBean, T. H. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301, 1882–1884 (2003).

    Article  CAS  Google Scholar 

  21. Park, S. H. et al. Programmable DNA self-assemblies for nanoscale organization of ligands and proteins. Nano Lett. 5, 729–733 (2005).

    Article  CAS  Google Scholar 

  22. Cohen, J. D., Sadowski, J. P. & Dervan, P. B. Addressing single molecules on DNA nanostructures. Angew. Chem. Int. Ed. 46, 7956–7959 (2007).

    Article  CAS  Google Scholar 

  23. Liu, Y., Lin, C., Li, H. & Yan, H. Aptamer-directed self-assembly of protein arrays on a DNA nanostructure. Angew. Chem. Int. Ed. 44, 4333–4338 (2005).

    Article  CAS  Google Scholar 

  24. Rinker, S., Ke, Y., Liu, Y., Chhabra, R. & Yan, H. Self-assembled DNA nanostructures for distance-dependent multivalent ligand–protein binding. Nature Nanotech. 3, 418–422 (2008).

  25. Fruk, L. et al. DNA-directed immobilization of horseradish peroxidase–DNA conjugates on microelectrode arrays: towards electrochemical screening of enzyme libraries. Chem. Eur. J. 13, 5223–5231 (2007).

    Article  CAS  Google Scholar 

  26. Cheglakov, Z., Weizmann, Y., Braunschweig, A. B., Wilner, O. I. & Willner, I. Increasing the complexity of periodic protein nanostructures by the rolling-circle-amplified synthesis of aptamers. Angew. Chem. Int. Ed. 47, 126–130 (2008).

    Article  CAS  Google Scholar 

  27. Weizmann, Y., Braunschweig, A. B., Wilner, O. I., Cheglakov, Z. & Willner, I. A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures. Proc. Natl Acad. Sci. USA 105, 5289–5294 (2008).

    Article  CAS  Google Scholar 

  28. Diehl, M. R., Zhang, K., Lee, H. J. & Tirrell, D. A. Engineering cooperativity in biomotor–protein assemblies. Science 311, 1468–1471 (2006).

    Article  CAS  Google Scholar 

  29. Bashor, C. J., Helman, N. C., Yan, S. & Lim, W. A. Using engineered scaffold interactions to reshape map kinase pathway signaling dynamics. Science 319, 1539–1543 (2008).

    Article  CAS  Google Scholar 

  30. Niemeyer, C. M., Koehler, J. & Wuerdemann, C. DNA-directed assembly of bienzymic complexes from in vivo biotinylated NAD(P)H:FMN oxidoreductase and luciferase. ChemBioChem 3, 242–245 (2002).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research is supported by the Converging Technologies Fund, administered by the Israel Science Foundation. We thank N. Melamed-Book from the Confocal Microscope Unit, Institute of Life Science, The Hebrew University of Jerusalem for experimental assistance.

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Authors and Affiliations

  1. Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel

    Ofer I. Wilner, Yossi Weizmann, Ron Gill, Oleg Lioubashevski, Ronit Freeman & Itamar Willner

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  1. Ofer I. Wilner
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  2. Yossi Weizmann
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  3. Ron Gill
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  4. Oleg Lioubashevski
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  5. Ronit Freeman
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  6. Itamar Willner
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Contributions

O.I.W. designed and performed the experiments, analysed the data and co-wrote the paper. Y.W. and R.G. contributed to the design of the systems and data analysis. O.L. contributed to the data analysis. R.F. participated in data analysis and co-wrote the paper, and I.W. contributed to the design of the systems, data analysis and co-writing of the paper.

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Correspondence to Itamar Willner.

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Wilner, O., Weizmann, Y., Gill, R. et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nature Nanotech 4, 249–254 (2009). https://doi.org/10.1038/nnano.2009.50

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