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Logical computation using algorithmic self-assembly of DNA triple-crossover molecules

Nature volume 407, pages 493–496 (2000)Cite this article

An Erratum to this article was published on 07 December 2000

Abstract

Recent work1,2,3 has demonstrated the self-assembly of designed periodic two-dimensional arrays composed of DNA tiles, in which the intermolecular contacts are directed by ‘sticky’ ends. In a mathematical context, aperiodic mosaics may be formed by the self-assembly of ‘Wang’ tiles4, a process that emulates the operation of a Turing machine. Macroscopic self-assembly has been used to perform computations5; there is also a logical equivalence between DNA sticky ends and Wang tile edges6,7. This suggests that the self-assembly of DNA-based tiles could be used to perform DNA-based computation8. Algorithmic aperiodic self-assembly requires greater fidelity than periodic self-assembly, because correct tiles must compete with partially correct tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules9 that can be used to execute four steps of a logical (cumulative XOR) operation on a string of binary bits.

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Figure 1: Calculation of cumulative XOR by self-assembly of DNA tiles.
Figure 2: Denaturing gels illustrating cumulative XOR calculations.

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Acknowledgements

We thank E. Winfree and A. Carbone for valuable discussions. This work has been supported by grants from DARPA and the National Science Foundation to J.H.R. and N.C.S.; ONR, USAF, NSF and NIH grants to N.C.S.; and NSF and ARO grants to J.H.R.

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Authors and Affiliations

  1. Department of Chemistry, New York University, New York, 10003, USA

    Chengde Mao & Nadrian C. Seeman

  2. Department of Computer Science, Duke University, Durham, 27707, North Carolina, USA

    Thomas H. LaBean & John H. Reif

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  1. Chengde Mao
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  2. Thomas H. LaBean
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  4. Nadrian C. Seeman
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Correspondence to Nadrian C. Seeman.

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Mao, C., LaBean, T., Reif, J. et al. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000). https://doi.org/10.1038/35035038

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