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Molecular implementation of simple logic programs

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Autonomous programmable computing devices made of biomolecules could interact with a biological environment and be used in future biological and medical applications1,2,3,4,5,6,7. Biomolecular implementations of finite automata8,9 and logic gates4,10,11,12,13 have already been developed14,15,16,17,18. Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions. Using molecular representations of facts such as Man(Socrates) and rules such as Mortal(X) ← Man(X) (Every Man is Mortal), the system can answer molecular queries such as Mortal(Socrates)? (Is Socrates Mortal?) and Mortal(X)? (Who is Mortal?). This biomolecular computing system compares favourably with previous approaches in terms of expressive power, performance and precision2,4,8,9,11,12,19. A compiler translates facts, rules and queries into their molecular representations and subsequently operates a robotic system that assembles the logical deductions and delivers the result. This prototype is the first simple programming language with a molecular-scale implementation.

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Figure 1: Molecular implementation of propositional logic statements and deductions.
Figure 2: Molecular implementation of simple logic programs.
Figure 3: Long deductions.
Figure 4: ‘Who is suitable for the army?’ and ‘Who is suitable for the academy?’.
Figure 5: Bottom-up deductions.

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  • 24 August 2009

    In the version of this Letter initially published online, the 'Query' that appeared in lines 1, 3, 5 and 7 of Fig. 3b was incorrect. This has been corrected for all versions of the Letter.


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We thank R. Adar, M. Kahan and B. Gil for their assistance and advice and A. Mishali and G. Brodsky for the preparation of the figures. This research was supported by The Israel Science Foundation grant no. 285/02, a research grant from the Clore Center for Biological Physics, a research grant from the Louis Chor Memorial Trust, a research grant from the Estate of Funnie Sherr, the Cymerman-Jubskind Prize, the Estate of Karl Felix Jakubskind and by the European Union FP7-ERC-AdG. S.K. is supported by the Yeshaya Horowitz association through the Center for Complexity Science. E.S. is the Incumbent of the Harry Weinrebe Professorial Chair of Computer Science and Biology and of the France Telecom–Orange Excellence Chair for Interdisciplinary Studies of the Paris ‘Centre de Recherche Interdisciplinaire’ (FTO/CRI).

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E.S. led the project. T.R. conceived the biomolecular design and the compiler and designed and performed the experiments. T.R. and S.K. wrote the analysis tools and automated the experimental protocols. T.R. and E.S. wrote the paper.

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Correspondence to Ehud Shapiro.

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Ran, T., Kaplan, S. & Shapiro, E. Molecular implementation of simple logic programs. Nature Nanotech 4, 642–648 (2009).

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