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Enzyme cascades activated on topologically programmed DNA scaffolds

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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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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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.

Corresponding author

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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