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DNA computing circuits using libraries of DNAzyme subunits

Nature Nanotechnology volume 5, pages 417–422 (2010)Cite this article

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A Corrigendum to this article was published on 09 February 2011

This article has been updated

Abstract

Biological systems that are capable of performing computational operations1,2,3 could be of use in bioengineering and nanomedicine4,5, and DNA and other biomolecules have already been used as active components in biocomputational circuits6,7,8,9,10,11,12,13. There have also been demonstrations of DNA/RNA-enzyme-based automatons12, logic control of gene expression14, and RNA systems for processing of intracellular information15,16. However, for biocomputational circuits to be useful for applications it will be necessary to develop a library of computing elements, to demonstrate the modular coupling of these elements, and to demonstrate that this approach is scalable. Here, we report the construction of a DNA-based computational platform that uses a library of catalytic nucleic acids (DNAzymes)10, and their substrates, for the input-guided dynamic assembly of a universal set of logic gates and a half-adder/half-subtractor system. We demonstrate multilayered gate cascades, fan-out gates and parallel logic gate operations. In response to input markers, the system can regulate the controlled expression of anti-sense molecules, or aptamers, that act as inhibitors for enzymes.

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Figure 1: Design of the DNA computing module.
Figure 2: Parallel activation of multigate systems.
Figure 3: Scalability of logic gates using gate cascades and fan-out.
Figure 4: Design of fan-out gates and the applicative of logic gates for nanomedicine.

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Change history

  • 09 February 2011

    In the version of this Letter originally published, components of the systems illustrated in Figs 3a–d, 4a and 4d were incorrectly labelled. In the Supplementary Information, components of the systems illustrated in Figs S7a, S9a–c and S10 were also incorrectly labelled. These errors have now been corrected in the HTML and PDF versions of the text, and in the Supplementary Information.

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Acknowledgements

Parts of this research are supported by the EC Project MOLOC and by the Office of Naval Research, USA. F.R. is Director of Research at Fonds National de la Recherche Scientifique (FNRS), Belgium. J.E. acknowledges a Converging Technologies Fellowship (Israel Science Foundation).

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Authors and Affiliations

  1. The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel

    Johann Elbaz, Oleg Lioubashevski, Fuan Wang, Raphael D. Levine & Itamar Willner

  2. Chemistry Department, B6c, University of Liège, Liège, 4000, Belgium

    Françoise Remacle

Authors
  1. Johann Elbaz
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  2. Oleg Lioubashevski
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  3. Fuan Wang
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  4. Françoise Remacle
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  5. Raphael D. Levine
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  6. Itamar Willner
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Contributions

J.E. designed the systems, performed the experiments, analysed the results and participated in the formulation of the paper. O.L. participated in designing the system, discussing the research results and the formulation of the paper. F.W. participated in designing the system and performed the experiments. R.D.L and F.R. participated in discussing the research results and the formulation of the paper. I.W. supervised the project, evaluated the research results and participated in the formulation of the paper.

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Correspondence to Itamar Willner.

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The authors declare no competing financial interests.

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Elbaz, J., Lioubashevski, O., Wang, F. et al. DNA computing circuits using libraries of DNAzyme subunits. Nature Nanotech 5, 417–422 (2010). https://doi.org/10.1038/nnano.2010.88

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